File: ChangeLog

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gmap 2010-07-21-1
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2010-07-21 08:17  twu

	* tests/setup1.test.in: Putting test chromosome in subdirectory

2010-07-21 08:17  twu

	* tests/setup2.test.in: Revised test for new gmapindex, but test
	  not being used currently

2010-07-21 08:13  twu

	* tests/iit.test.in: Not testing for diff in iittest.iit

2010-07-21 08:12  twu

	* tests/: align.test.ok, coords1.test.ok, map.test.ok: Changed
	  expectations to match latest program output

2010-07-21 08:11  twu

	* tests/iittest.iit.ok: Using latest IIT version

2010-07-21 08:10  twu

	* tests/Makefile.am: Using ref3offsets and ref3positions instead of
	  idxoffsets and idxpositions

2010-07-21 08:09  twu

	* config/: acx_mmap_fixed.m4, acx_mmap_variable.m4: Added stdlib.h
	  and unistd.h headers

2010-07-21 08:08  twu

	* config.site.rescomp.prd, config.site.rescomp.tst: Initial import
	  into CVS

2010-07-21 08:08  twu

	* config.site.gne: Removed old config file

2010-07-21 08:06  twu

	* acinclude.m4: Including builtin m4 code

2010-07-21 08:06  twu

	* MAINTAINER: Added notes about checking Bigendian behavior

2010-07-21 08:06  twu

	* share/: archive.html, index.html: Revised for 2010-07-20 release

2010-07-21 08:05  twu

	* configure.ac: Better checking for VERSION

2010-07-21 08:04  twu

	* bootstrap.dna, bootstrap.gsnaptoo, bootstrap.three: Initial
	  import into CVS

2010-07-21 08:03  twu

	* bootstrap.pmaptoo: Added --force flag

2010-07-21 08:03  twu

	* bootstrap.gmaponly: Added autoreconf step

2010-07-21 08:02  twu

	* README, VERSION: Changed for 2010-07-20 release

2010-07-21 08:02  twu

	* util/gmap_process.pl.in: Removed check for contig version

2010-07-21 08:01  twu

	* util/gmap_update.pl.in: Not updating chromosome or contig IIT
	  files

2010-07-21 08:01  twu

	* util/gmap_setup.pl.in: Providing -q and -Q flags for GMAP and
	  PMAP indexing intervals.

2010-07-21 07:53  twu

	* util/: gsnap-fetch-reads.pl, gsnap-fetch-reads.pl.in,
	  gsnap-remap.pl, gsnap-remap.pl.in: Initial import into CVS

2010-07-21 07:53  twu

	* util/gsnap_splicing.pl: Program is superseded by C program
	  gsnap_splices

2010-07-21 07:52  twu

	* util/gsnap_splicing.pl: Various changes.  Program is superseded
	  by C program gsnap_splices.

2010-07-21 07:51  twu

	* util/: gmap_compress.pl.in, gmap_reassemble.pl.in,
	  gmap_uncompress.pl.in, md_coords.pl.in: Using "use warnings"
	  instead of "-w" flag

2010-07-21 07:49  twu

	* util/fa_coords.pl.in: Handling duplicate occurrences of a
	  chromosome.  Limiting number of warnings.

2010-07-21 07:48  twu

	* util/Makefile.am: Added gmap_update

2010-07-21 07:46  twu

	* src/: pair.c, pair.h, stage3.c, stage3.h, gmap.c: Implemented -f
	  4 GFF estmatch format based on patch from Shaun Jackman and
	  Eoghan Harrington of British Columbia Genome Sciences Centre.

2010-07-21 07:32  twu

	* src/chimera.c: Commented out problematic code, to be resolved
	  later

2010-07-21 07:32  twu

	* src/get-genome.c: Fixed coordinates when retrieving map file
	  contents

2010-07-21 06:27  twu

	* src/: splicegraph.c, tallyadd.c, tallygene.c, tallystrand.c:
	  Initial import into CVS

2010-07-21 06:23  twu

	* src/: cum.c, dibaseindex.c, geneadjust.c, pairingtrain.c: Initial
	  import into CVS

2010-07-21 06:20  twu

	* src/tallyhmm.c: Using new Parserange_universal function

2010-07-21 06:19  twu

	* src/: tally.c, tally.h: Treating counts as long ints

2010-07-21 06:19  twu

	* src/splicegene.c: Changed algorithm

2010-07-21 06:18  twu

	* src/spliceeval.c: Removed unused code

2010-07-21 06:17  twu

	* src/: plotgenes.c, plotgenes.h: Several changes, including trying
	  to resolve fatal errors

2010-07-21 06:15  twu

	* src/: pdldata.c, pdldata.h: Implemented Pdldata_new and
	  Pdldata_write

2010-07-21 06:15  twu

	* src/pairingstrand.c: Using new Parserange_universal function

2010-07-21 06:14  twu

	* src/pairinggene.c: Counting found splices as flats

2010-07-21 06:14  twu

	* src/pairingflats.c: Changed algorithm for finding flat regions

2010-07-21 06:14  twu

	* src/pairingcum.c: Treating high and low reads separately

2010-07-21 06:13  twu

	* src/oligo-count.c: Using new interface to Reader_new.

2010-07-21 04:31  twu

	* src/: lgamma.c, lgamma.h: Handling counts as long ints

2010-07-21 04:29  twu

	* src/: hint.h, hint.c: Changed models

2010-07-21 04:28  twu

	* src/geneeval.c: Using new Parserange_universal function

2010-07-21 04:13  twu

	* src/genecompare.c: Separate output for forward and reverse
	  chromosome strands.

2010-07-21 04:12  twu

	* src/gdiag.c: Removed some output.  Using new interfaces to
	  IIT_read.

2010-07-21 03:16  twu

	* src/: dibase.c, dibase.h, exonscan.c: Change in algorithm

2010-07-21 03:16  twu

	* src/chimera.c: Using Path_matchscores instead of
	  Stage3_matchscores

2010-07-21 03:14  twu

	* src/cappaths.c: Using xintercepts instead of slopes

2010-07-21 03:13  twu

	* src/: boyer-moore.c, boyer-moore.h: Added procedures for
	  chop_primers.c

2010-07-21 03:12  twu

	* src/add_rpk.c: Change of output format

2010-07-20 09:00  twu

	* src/stage1hr.c: Tightened requirements further for splice site
	  probabilities on distant splicing.

2010-07-20 07:36  twu

	* src/stage3hr.c: Using nmatches to filter pairs containing
	  terminal alignments

2010-07-20 07:35  twu

	* src/gsnap.c: Changed advice on RNA-Seq settings for -m.

2010-07-20 06:10  twu

	* share/: archive.html, index.html: Released version 2010-03-10

2010-07-20 06:05  twu

	* src/: substring.c, substring.h: Computing nmatches directly

2010-07-20 06:04  twu

	* src/stage3hr.h: Removed score parameter from Stage3_new_terminal

2010-07-20 06:04  twu

	* src/stage3hr.c: Selecting best among terminal alignments.
	  Computing nmatches directly.

2010-07-20 06:04  twu

	* src/stage1hr.c: Changed algorithm for finding terminal
	  alignments.  Requiring distant splicing to have high splice
	  probabilities.

2010-07-20 06:03  twu

	* src/sam_splices.c: Computing readlengths on each end of splice
	  separately

2010-07-20 06:02  twu

	* src/: gsnap.c, gsnap_splices.c: Added debugging code

2010-07-19 06:31  twu

	* src/stage1hr.c: Using sequences as numeric in some cases

2010-07-19 06:29  twu

	* src/: maxent.c, maxent.h: Added procedures to handle sequences as
	  numeric

2010-07-19 06:28  twu

	* src/gsnap.c: Added a comment to the --help message

2010-07-19 06:27  twu

	* src/: genome_hr.c, genome_hr.h: Added a procedure to retrieve a
	  dinucleotide

2010-07-19 06:27  twu

	* src/: genome.c, genome.h: Added a procedure to retrieve sequences
	  as numeric

2010-07-19 06:25  twu

	* src/: Makefile.pmaptoo.am, Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am: Revised files and programs as needed

2010-07-16 08:21  twu

	* src/stage3hr.c: Requiring that dual translocations be concordant
	  only across the same two chromosomes.

2010-07-16 08:20  twu

	* src/smooth.c: Conserving listcells where possible

2010-07-16 08:19  twu

	* src/: oligoindex.c, oligoindex.h: Removed computation of
	  fingerprint

2010-07-16 08:19  twu

	* src/: list.c, list.h: Implemented List_transfer_one and
	  List_push_existing

2010-07-16 08:18  twu

	* src/gsnap.c: Performing trimming by default

2010-07-16 08:18  twu

	* src/dynprog.c: Ensuring that finalscore is assigned in
	  Dynprog_genome_gap.

2010-07-16 07:55  twu

	* src/: substring.h, stage3hr.c, substring.c: Providing a minlength
	  parameter to Substring_new, so end indels do not get eliminated.

2010-07-16 07:10  twu

	* src/chop_primers.c: Initial import into CVS

2010-07-16 06:21  twu

	* src/sam_tally.c: Trimming uses -3 for mismatches and resets
	  negative scores to zero.  Handling hard clipping.

2010-07-16 06:20  twu

	* src/gsnap_tally.c: Trimming uses -3 for mismatches and resets
	  negative scores to zero

2010-07-16 06:19  twu

	* src/gsnap_splices.c: Sorting splices using both ends.

2010-07-16 06:19  twu

	* src/sam_splices.c: Handling AT-AC introns.  Sorting splices using
	  both ends.

2010-07-16 06:18  twu

	* src/: samread.c, samread.h: Returning acc in parsing line

2010-07-16 06:18  twu

	* src/sam.h: Renamed NOT_PRIMARY bit

2010-07-16 06:17  twu

	* src/sam.c: Implemented hard clipping of sequences for SAM output.
	  Enabled printing of distant splices onto two separate lines.
	  Using NOT_PRIMARY bit in flag.

2010-07-16 06:16  twu

	* src/: sequence.c, sequence.h: Implemented hard clipping of
	  sequences for SAM output

2010-07-16 06:15  twu

	* src/stage3.c: Removed unused procedures.  Conserving listcells
	  when possible.

2010-07-16 06:14  twu

	* src/stage2.c: Removed unused procedures

2010-07-16 06:13  twu

	* src/gmap.c: Removed references to Intpool_T

2010-07-16 06:12  twu

	* src/pairpool.c: Setting initial value for state

2010-07-16 06:11  twu

	* src/: matchpool.c, matchpool.h: Implemented Matchpool_free_memory
	  procedure

2010-07-16 06:10  twu

	* src/: mem.c, mem.h: Added procedures for computing memory usage

2010-07-16 06:06  twu

	* src/: stage3hr.c, substring.c, substring.h: Now trimming from
	  both ends of terminal alignment.  Explicitly specifying which
	  ends to trim.

2010-07-16 05:28  twu

	* src/substring.h: Replaced Substring_T with T

2010-07-16 05:28  twu

	* src/substring.c: Allowing Substring_new to return NULL if trimmed
	  alignments are poor.	Replaced Substring_T with T.  Resetting
	  score to zero when it becomes negative in trimming.

2010-07-16 05:27  twu

	* src/: stage1hr.c, stage3hr.c: Allowing Substring_new and
	  Stage3_new to return NULL if trimmed alignments are poor.

2010-07-16 00:40  twu

	* src/substring.c: Changed mismatch score from -1 to -3 for
	  trimming

2010-07-16 00:33  twu

	* src/: stage3hr.h, stage1hr.c: Added notion of ambiguous splices.

2010-07-16 00:32  twu

	* src/stage3hr.c: Added notion of ambiguous splices.  Fixing
	  removal of duplicates.

2010-07-14 14:47  twu

	* src/: stage3hr.c, stage3hr.h: Implemented Stage3_substring_low

2010-07-14 14:46  twu

	* src/samread.c: Added debugging comments

2010-07-14 14:46  twu

	* src/: sam.c, sam.h: Moved flag constants to sam.h.  Using
	  Stage3_substring_low to print chromosomal pos.

2010-07-14 14:45  twu

	* src/sam_splices.c: Simplified loop

2010-07-14 14:44  twu

	* src/gsnap_splices.c: Having lines_gc return NULL

2010-07-14 14:44  twu

	* src/gsnap_tally.c: Fixed trimming.  Turning off trimming by
	  default.

2010-07-14 14:43  twu

	* src/sam_tally.c: Initial import into CVS

2010-07-14 05:04  twu

	* src/: sam_splices.c, samread.c, samread.h: Fixed bug in
	  specifying allowed dinucleotides.  Moved parsing procedures to
	  samread.c.

2010-07-12 22:31  twu

	* src/sam_splices.c: Initial import into CVS

2010-07-10 11:19  twu

	* src/spliceclean.c: Changed variable names

2010-07-10 05:21  twu

	* src/: stage2.c, stage2.h, stage3.h: Removed stage2 fingerprint

2010-07-10 05:20  twu

	* src/gmap.c: Added freeing of pairpool and diagpool memory at
	  certain intervals.

2010-07-10 05:18  twu

	* src/: stage3.c, pair.c, pair.h: Moved HMM code from pair.c to
	  stage3.c

2010-07-10 05:16  twu

	* src/: pairpool.c, pairpool.h: Implemented Pairpool_free_memory
	  function

2010-07-10 05:16  twu

	* src/: diagpool.c, diagpool.h: Implemented Diagpool_free_memory
	  function

2010-07-10 01:59  twu

	* src/gsnap.c: Added ability to remove adapters from paired-end
	  reads.  Providing option for maxlength on trimming.

2010-07-10 01:58  twu

	* src/gmap.c: Using Stage2_scan method to rank gregions.  Providing
	  additional diagnostic options.

2010-07-10 01:42  twu

	* src/: diag.c, diag.h, diagpool.h: Added ability to allocate
	  memory for diagonals, rather than using diagpool

2010-07-10 01:38  twu

	* src/tally_expr.c: Fixed bug in using IIT index

2010-07-10 01:35  twu

	* src/substring.h: Added handling of terminal reads

2010-07-10 01:34  twu

	* src/substring.c: Using trimming maxlength.  Fixed printing of
	  sequences with adapters.

2010-07-10 01:30  twu

	* src/stage3hr.c: Fixed identification of duplicates.  Using total
	  matches to compare results, rather than score.

2010-07-10 01:29  twu

	* src/: stage3.c, stage3.h: Using an HMM to find bad sections and
	  fixing resulting dual breaks.

2010-07-10 01:27  twu

	* src/: stage2.c, stage2.h: Added Stage2_scan procedure.  Providing
	  diagonals for diagnostic purposes.  Computing a fingerprint.

2010-07-10 01:23  twu

	* src/stage1.c: Using a boolean to see if weight exists rather than
	  depending on floating point value

2010-07-10 01:19  twu

	* src/sequence.h: Added handling of finding adapters.  Computing
	  sequence quality for trimming.

2010-07-10 01:03  twu

	* src/sequence.c: Fixed bug where fastq quality line begins with
	  ">".	Added removal of adapters from paired-end data.

2010-07-10 00:59  twu

	* src/sam.h: Removed genome from argument lists

2010-07-10 00:57  twu

	* src/sam.c: Fixed bugs in coordinates, epecially involving trimmed
	  reads.  Handling terminal reads.

2010-07-10 00:51  twu

	* src/: result.c, result.h: Added ability to report intermediate
	  gregions or diagonals

2010-07-10 00:02  twu

	* src/oligoindex.h: Added computation of fingerprint

2010-07-09 23:57  twu

	* src/oligoindex.c: Added necessary clearing of oligoindex.

2010-07-09 11:38  twu

	* src/: pairdef.h, pairpool.c: Added Pair_goodness_hmm procedure.

2010-07-09 11:38  twu

	* src/: pair.c, pair.h: Added Pair_goodness_hmm procedure.  Added
	  printing of stage2 fingerprint.

2010-07-09 11:37  twu

	* src/orderstat.c: Removed reliance on a floating point equality

2010-07-09 11:36  twu

	* src/: mem.c, mem.h: Added leak check procedures

2010-07-09 11:35  twu

	* src/: match.c, match.h, matchdef.h: Using a boolean to record
	  whether weight is zero or not, rather than relying on floating
	  point

2010-07-09 11:34  twu

	* src/indexdb_hr.c: Added comment

2010-07-09 11:34  twu

	* src/indexdb.c: Fixed printf procedure

2010-07-09 11:34  twu

	* src/iit-read.h: Removed unused IIT_print prototype

2010-07-09 11:33  twu

	* src/iit-read.c: Fixed print_record procedure

2010-07-09 11:32  twu

	* src/gsnap_tally.c: Fixed trimming procedure.	Added reference
	  nucleotide in all lines.  Fixed processing of all chromosomes.

2010-07-09 11:31  twu

	* src/gsnap_splices.c: Fixed parsing.  Made uniquep false by
	  default.  Added info about nextensions and nunique.

2010-07-09 11:28  twu

	* src/: gregion.c, gregion.h: Added fields ncovered and source,
	  plus function Gregion_cmp

2010-07-09 11:28  twu

	* src/get-genome.c: Removed unused function print_map

2010-07-09 11:27  twu

	* src/: genome.c, genome.h: Added function Genome_get_char

2010-07-09 11:27  twu

	* src/dynprog.c: Added space for formatting

2010-07-09 11:16  twu

	* src/stage1hr.h: Setting a maxlength on trimming

2010-07-09 11:12  twu

	* src/stage1hr.c: Finding terminals rather than halfintrons.  Fixed
	  case where splice ends are adjacent in genome.

2010-07-02 08:53  twu

	* src/stage3hr.h: Added support for a terminal alignment.

2010-07-02 08:53  twu

	* src/stage3hr.c: Added support for a terminal alignment.  Removed
	  halfintron_support field.

2010-05-28 05:17  twu

	* src/iit_store.c: Fixed issues with removing and re-inserting null
	  divstring.

2010-05-26 07:13  twu

	* src/stage1hr.c: Added trim_maxlength.  Added nmismatches to
	  halfintron alignments.

2010-05-26 06:00  twu

	* src/stage3hr.h: Added trim_maxlength.

2010-05-26 06:00  twu

	* src/stage3hr.c: Added trim_maxlength.  Checking pairlength on
	  samechr_single to see if concordant.

2010-05-21 08:17  twu

	* src/: iit-read.c, iit-read.h, stage3.c: Fixed printing of
	  chromosome in map results

2010-05-20 07:51  twu

	* src/stage3hr.c: Finding concordant pairs against translocations
	  with chrnum == 0, by making copies for each chrnum and storing in
	  effective_chrnum.

2010-05-17 04:08  twu

	* src/: substring.c, substring.h: Added halfintron support field.

2010-05-17 04:06  twu

	* src/: stage3hr.c, stage3hr.h: Implemented sense consistency in
	  paired-end alignments

2010-05-17 04:05  twu

	* src/stage1hr.c: Fixed bugs in previous implementation of half
	  introns

2010-05-16 08:04  twu

	* src/: stage1hr.c, stage3hr.c: Implemented new way of handling
	  half introns, by storing best half intron for sense and for
	  antisense

2010-05-14 02:00  twu

	* src/: stage1hr.c, stage3hr.c, stage3hr.h, resulthr.c, resulthr.h:
	  Added procedure for finding samechr pairs if no concordant ones
	  found.  Revised result types to include PAIREDEND_SAMECHR_SINGLE
	  and PAIREDEND_SAMECHR_MULTIPLE.

2010-05-13 07:52  twu

	* src/stage1hr.c: Added conditional compilation statements for
	  filtering halfintrons

2010-05-13 07:51  twu

	* src/: gsnap.c, stage3hr.c, stage3hr.h: Handling failsonly and
	  nofails flags for paired-end data.  Printing FASTQ format for
	  failsonly on single-end data.

2010-04-16 10:31  twu

	* src/iit-write.c: Fixed bug in freeing data when number of
	  intervals is zero

2010-04-12 07:23  twu

	* src/iit-read.c: Commented out IIT_index function

2010-04-12 02:38  twu

	* src/sam.c: Fixed situation where query has no mapping and mate is
	  an interchromosomal splice

2010-04-05 07:17  twu

	* src/tally_expr.c: Initial import into CVS

2010-04-02 03:20  twu

	* src/iit_get.c: Added allele information to -T option

2010-03-24 09:23  twu

	* src/gmap.c: Using new interface to blackboard.c

2010-03-24 09:22  twu

	* src/: blackboard.c, blackboard.h: Added input2 to Blackboard_T
	  object

2010-03-24 09:22  twu

	* src/: gsnap.c, sequence.c, sequence.h: Implemented processing of
	  FASTQ files

2010-03-24 09:21  twu

	* src/: stage3hr.c, stage3hr.h: Fixed classification of paired-end
	  reads when one or both ends have a translocation.

2010-03-09 09:34  twu

	* src/stage3hr.c: Revised half_intron_score.  Using that score when
	  comparing overlapping half_introns with one another.

2010-03-09 09:32  twu

	* src/: gsnap.c, stage1hr.c, stage1hr.h: Added parameter for
	  min_distantsplicing_identity

2010-03-09 06:27  twu

	* src/stage1hr.c: Providing querylength information when making
	  Stage3_T splice objects

2010-03-09 06:26  twu

	* src/: stage3hr.c, stage3hr.h: Adding a penalty to half-intron
	  alignments based on the amount of sequence that was not aligned.

2010-03-09 05:17  twu

	* src/stage3hr.c: Changed output for samechr results

2010-03-09 04:25  twu

	* src/substring.c: Printing sub:0 instead of exact

2010-03-09 04:25  twu

	* src/stage1hr.c: Checking for exact matches that cross chromosomal
	  boundaries

2010-03-08 04:25  twu

	* src/resulthr.c: Making all paired reads of type concordant

2010-03-08 04:23  twu

	* src/stage3hr.c: Added printing of samechr as a special case of
	  PAIREDEND_AS_SINGLES_UNIQUE.

2010-03-08 04:22  twu

	* src/sam.h: Added mate information to nomapping result.

2010-03-08 04:22  twu

	* src/sam.c: Removed unused code.  Fixed printing of query string.
	  Added mate information to nomapping result.

2010-03-08 04:21  twu

	* src/gsnap_tally.c: Handling new output format for GSNAP

2010-03-08 04:20  twu

	* src/gsnap.c: Using new interface for SAM_print_nomapping

2010-03-08 04:18  twu

	* README: Added more information about GSNAP features and output

2010-03-04 13:53  twu

	* src/: iit-read.c, iit-read.h: Added function IIT_dump_sam

2010-03-04 13:52  twu

	* src/gsnap.c: Renamed resulttypes

2010-03-04 13:52  twu

	* src/: resulthr.c, resulthr.h: Added resulttype
	  PAIREDEND_AS_SINGLES_UNIQUE

2010-03-04 13:51  twu

	* src/: substring.c, substring.h: Added function
	  Substring_match_length

2010-03-04 13:51  twu

	* src/stage3hr.h: Computing chrnum, chroffset, genomicstart, and
	  genomicpos at Stage3_T level for splices.

2010-03-04 13:51  twu

	* src/stage3hr.c: Pairing up at each successive score level.
	  Computing chrnum, chroffset, genomicstart, and genomicpos at
	  Stage3_T level for splices.

2010-03-04 13:49  twu

	* src/stage1hr.c: Fixed bug allowing deletion to extend past
	  genomicpos 0.  Fixed cases where known splicing occurs near end
	  of sequence.	Removing duplicate hits before pairing up ends.

2010-03-04 13:45  twu

	* src/sam.c: Made multiple changes to generate correct SAM output

2010-03-01 00:29  twu

	* src/: substring.c, substring.h: Removed unnecessary parameters
	  during printing

2010-03-01 00:29  twu

	* src/stage3hr.h: Removed unnecessary parameters.

2010-03-01 00:28  twu

	* src/stage3hr.c: Added support information to splices, and using
	  it to select best half introns.  Removing unnecessary parameters
	  during printing.  Checking for abort in pairing process, based on
	  local counts.

2010-03-01 00:26  twu

	* src/stage1hr.c: Added support information in making splices.	Not
	  checking for sufficiency for half introns.  Using an
	  abort_pairing_p flag, and when true, recomputing ends as singles.

2010-03-01 00:24  twu

	* src/splicing-score.c: Using parserange module.  Allowing range to
	  be specified.

2010-03-01 00:24  twu

	* src/iit-read.h: Removed unused parameter

2010-03-01 00:23  twu

	* src/iit-read.c: Changed format strings to eliminate compiler
	  warnings

2010-03-01 00:23  twu

	* src/genome.c: Added parentheses around some conditional
	  statements

2010-02-26 07:11  twu

	* src/stage3.c: Removed unused parameters from print functions

2010-02-26 07:11  twu

	* src/sequence.c: Handling sequence at end of file without line
	  feed

2010-02-26 07:10  twu

	* src/reader.c: Commented out unused code

2010-02-26 07:10  twu

	* src/gsnap.c: Added flags for SAM and quiet-if-excessive.  Dropped
	  flags for probability thresholds.

2010-02-26 07:09  twu

	* src/datadir.h: Added external interface for a function

2010-02-25 09:34  twu

	* src/sam.c: Fixed bug where numbers of deletions was being
	  reported as a negative number

2010-02-25 09:11  twu

	* src/: genome_hr.c, genome_hr.h, stage1hr.c: Removed computation
	  of snpdiffs by genome_hr

2010-02-25 01:58  twu

	* src/genome_hr.h: Added code for performing trimming.	Using
	  macros for clearing and setting outside regions in start and end
	  blocks.

2010-02-25 01:52  twu

	* src/genome_hr.c: Added code for performing trimming.	Using
	  macros for clearing and setting outside regions in start and end
	  blocks.

2010-02-25 01:50  twu

	* src/stage1hr.c: Added trimming of splice ends to avoid extending
	  into region of many mismatches.  Saving all splice ends that have
	  sufficient sequence and probability support.

2010-02-23 02:37  twu

	* src/substring.c: Fixed printing of splices.  Fixed bugs in
	  retrieving SNP information.

2010-02-23 02:35  twu

	* src/stage3hr.h: Returning found score from all functions that
	  create a Stage3_T object

2010-02-23 02:35  twu

	* src/stage3hr.c: Fixed computation of pair length.  Fixed search
	  for concordant pairs.

2010-02-23 02:33  twu

	* src/stage1hr.h: Removed unused parameters

2010-02-23 02:33  twu

	* src/stage1hr.c: Using found score rather than found number of
	  mismatches.  Fixed cases where indel pos was outside of query
	  range.

2010-02-23 02:30  twu

	* src/spanningelt.c: Fixed typecast error

2010-02-23 02:30  twu

	* src/: sam.c, sam.h: Implemented SAM output for paired-end reads

2010-02-12 09:03  twu

	* src/: substring.c, substring.h, resulthr.c, resulthr.h,
	  stage1hr.c, stage3hr.c, stage3hr.h: Changed output format to have
	  separate columns for alignment information and pair information.
	  Standardized output routines.  Three categories for paired-end
	  reads: concordant, samechr, and unpaired.

2010-02-11 09:54  twu

	* src/: stage1hr.c, sam.c, sam.h, stage3hr.c, stage3hr.h,
	  substring.c, substring.h: Rearranged and cleaned up code for
	  making substrings

2010-02-10 00:55  twu

	* util/gmap_process.pl.in: Removed code that removed version
	  numbers on accessions

2010-02-03 03:07  twu

	* src/indexdb.c: Fixed string formatting

2010-02-03 02:53  twu

	* src/snpindex.c: Fixed some printing statements

2010-02-03 02:37  twu

	* src/get-genome.c: Changed call to parserange to match new
	  interface

2010-02-03 02:19  twu

	* src/: uintlist.c, uintlist.h: Added Uintlist_find command

2010-02-03 02:18  twu

	* src/: table.c, tableint.c: Added stdlib.h header file

2010-02-03 02:18  twu

	* src/stage3.h: Added genome to print_alignment for splice sites
	  scores in output

2010-02-03 02:18  twu

	* src/stage3.c: Allowing null gaps again

2010-02-03 02:16  twu

	* src/stage2.c: Added separate data types for a 1-dimensional
	  matrix and 2-dimensional matrix representation

2010-02-03 02:16  twu

	* src/stage1hr.c: Prevented splicing unless both dinucleotides are
	  present

2010-02-03 02:15  twu

	* src/stage1.c: Removed extensions of gregions

2010-02-03 02:14  twu

	* src/sequence.c: Commented out unused functions

2010-02-03 02:14  twu

	* src/: resulthr.c, resulthr.h: Renamed result type to
	  PAIRED_AND_PAIRABLE

2010-02-03 02:13  twu

	* src/: parserange.c, parserange.h: Implemented parse_query
	  function

2010-02-03 02:12  twu

	* src/: pair.c, pair.h: Added donor and acceptor scores to output

2010-02-03 02:12  twu

	* src/: orderstat.c, orderstat.h: Added functions for long int

2010-02-03 02:12  twu

	* src/: oligoindex.c, oligoindex.h: Added parameter oned_matrix_p

2010-02-03 02:11  twu

	* src/nr-x.h: Added ppois functions

2010-02-03 02:11  twu

	* src/nr-x.c: Added ppois functions.  Fixed bug in pbinom for zero
	  observed counts.

2010-02-03 02:10  twu

	* src/: list.h, list.c: Rewrote function for List_insert

2010-02-03 02:09  twu

	* src/intlist.c: Handling case of empty list better for conversion
	  to string

2010-02-03 02:08  twu

	* src/: interval.c, interval.h: Added functions for sorting
	  intervals by position

2010-02-03 02:08  twu

	* src/indexdb.c: Added debugging statements

2010-02-03 02:07  twu

	* src/iit_plot.c: Using new interface to Genome_new

2010-02-03 02:07  twu

	* src/iit_get.c: Implemented statistics function.  Using long int
	  for tally IITs.  Using parserange module.

2010-02-03 02:06  twu

	* src/iit-read.h: Added function for divlength

2010-02-03 02:05  twu

	* src/iit-read.c: New implementation of sorting of intervals by
	  position

2010-02-02 10:14  twu

	* src/gmapindex.c: Increased expected table size for number of
	  chromosomes.	Stopping warning messages after 100 printed.

2010-02-02 10:13  twu

	* src/gmap.c: Added genome parameter to Stage3_print_alignment

2010-02-02 10:12  twu

	* src/get-genome.c: Using parserange module.  Implemented flanking
	  segments.

2010-02-02 10:11  twu

	* src/genome_hr.c: Removed unused variables for certain
	  compile-time conditions

2010-02-02 10:10  twu

	* src/genome-write.c: Stopping warning messages after 50 are
	  printed

2010-02-02 10:10  twu

	* src/gdiag.c: Formatting changes

2010-02-02 10:10  twu

	* src/except.c: Using pointers to exception frame objects

2010-02-02 09:58  twu

	* src/dynprog.c: Reduced PAIRED_OPEN penalty from -24 to -18

2010-02-02 09:57  twu

	* src/diag.h: Added function Diag_range

2010-02-02 09:57  twu

	* src/diag.c: Reduced EXTRA_BOUNDS parameter

2010-02-02 09:57  twu

	* src/datadir.c: Fixed bug where insufficient buffer space was
	  provided for one string

2010-02-02 09:55  twu

	* src/backtranslation.h: Removed void in formal parameter lists

2010-02-02 09:55  twu

	* src/backtranslation.c: Casting character array indices to ints

2010-02-02 02:31  twu

	* src/splicegene.c: Attempted to find genebounds on all sites

2010-02-01 04:33  twu

	* src/splicegene.c: Implemented finding and reporting of alternate
	  splice forms

2010-01-31 23:08  twu

	* src/splicegene.c: Differentiated donor and acceptor sites.
	  Handling reverse strand in reverse direction.  Noting conflicts
	  when either endpoint is close to an endpoint on the other.

2010-01-31 07:04  twu

	* src/splicegene.c: Completely new rewrite based on pairinggene.c.
	  Attempt to assign genebounds based on tally high and tally low.

2010-01-30 07:29  twu

	* src/splicegene.c: Using tally high and low.  Added hooks for
	  alternate splice site.

2010-01-30 06:27  twu

	* src/spliceclean.c: Performing validation based on ratio of count
	  to maxcount over region

2010-01-29 07:16  twu

	* src/spliceclean.c: Using less memory.  Attempted validation of
	  splices based on envelope.

2010-01-29 03:12  twu

	* src/spliceclean.c: Initial import into CVS

2010-01-29 00:58  twu

	* src/pairingcum.c: Implemented filtering based on significance at
	  endpoints

2010-01-27 11:09  twu

	* src/pairingcum.c: Added computation on floors as well as ceilings

2010-01-24 21:08  twu

	* src/pairinggene.c: Testing flat regions against the splice IIT to
	  determine if they are intron-like.  Also adding splice edges to
	  the original list.  Splices will therefore need to be filtered.

2010-01-24 18:21  twu

	* src/pairinggene.c: Reverted to previous version using only
	  observed GSNAP splices

2010-01-24 17:51  twu

	* src/pairinggene.c: Improved algorithm for distinguishing between
	  intergenic flats and intron flats.

2010-01-24 12:44  twu

	* src/geneeval.c: Initial import into CVS

2010-01-24 12:38  twu

	* src/pairinggene.c: Improved algorithm for detecting intergenic
	  regions.  For flats, we can use a loose criterion without a level
	  threshold, because of the ordering constraint.  We are using both
	  edges from flats and from gsnap splices.  We added a procedure
	  for distinguishing between intergenic regions and long exons
	  based on the counts_tally.

2010-01-24 05:59  twu

	* src/pairinggene.c: Using iblocks instead of nblocks to control
	  exon segments, so essentially all combinations of introns are
	  considered

2010-01-24 05:00  twu

	* src/pairinggene.c: Reading in edges from the splices_iit file,
	  presumably after filtering

2010-01-24 02:15  twu

	* src/pairinggene.c: Attempt to get more edges by looking up splice
	  edges when a flat does not yield clean ones

2010-01-23 19:23  twu

	* src/cappaths.c: Added analysis of slopes and attempt to find a
	  flat region

2010-01-23 19:20  twu

	* src/pairinggene.c: Fixed bug with negative unsigned int

2010-01-23 18:54  twu

	* src/pairinggene.c: For objective function, using the count of
	  observed splices from GSNAP.

2010-01-23 17:50  twu

	* src/pairinggene.c: Eliminated concept of an eblock (or exon
	  block).  Trying all intron combinations, since intergenic blocks
	  are sufficient to contain the search space.

2010-01-23 17:31  twu

	* src/pairinggene.c: Fixed bug where an up was a terminal, which
	  hid the downstream down.  Added some debugging code.

2010-01-23 16:26  twu

	* src/pairinggene.c: Added checking of edges based on genome splice
	  sites

2010-01-23 14:34  twu

	* src/pairinggene.c: Made intergenic regions go between flats, and
	  increased the length requirement.  Using auto_exonlength for
	  adding exons.

2010-01-23 13:30  twu

	* src/pairinggene.c: Restricted intergenic blocks to be between
	  adjacent down to up edges

2010-01-23 11:45  twu

	* src/pairinggene.c: Reordered procedures to minimize memory usage

2010-01-23 09:14  twu

	* src/pairinggene.c: Implemented a new algorithm for constructing
	  the graph, using various blocks and building the graph in stages

2010-01-23 09:09  twu

	* src/tally.c: Added functions for the median and for adding a
	  runlength to an existing count

2010-01-23 05:38  twu

	* src/pairinggene.c: Fixed error in formula for computing down edge

2010-01-22 23:48  twu

	* src/splicing-score.c: Initial import into CVS

2010-01-22 23:35  twu

	* src/pairingcum.c: Fixed a bug where the cum was being put at the
	  wrong position, causing the down edge to be 1 position too small.

2010-01-22 18:29  twu

	* src/pairinggene.c: Implemented trimming of ends

2010-01-22 16:22  twu

	* src/pairinggene.c: Implemented a new test for intergenic regions
	  based on finding a long flat region in the counts, which should
	  not happen in an exon.

2010-01-22 15:10  twu

	* src/pairinggene.c: Added a test for sharpness based on an area
	  ratio

2010-01-22 13:51  twu

	* src/pairinggene.c: Fixed dynamic programming procedure

2010-01-22 13:02  twu

	* src/pairinggene.c: Keeping a min-max test on whether introns are
	  acceptable, but using mean levels of introns and exons for
	  scoring.

2010-01-22 12:48  twu

	* src/pairinggene.c: Using zero-based check on pairingfull to test
	  for intergenic regions.  Added a greedy addition of introns.

2010-01-22 10:34  twu

	* src/pairinggene.c: Attempt to use pairing full information and
	  gradual downsloping to find UTRs.

2010-01-22 04:43  twu

	* src/pairinggene.c: Using intron level minus exon level to
	  determine edges with greater sensitivity.  Implemented scores as
	  double, rather than int, although currently using mincount and
	  maxcount.

2010-01-22 01:51  twu

	* src/pairinggene.c: Changed from onepath dynamic programming to
	  multiple paths with terminals.  Using explicit objects for exons
	  and introns.

2010-01-21 16:50  twu

	* src/pairinggene.c: Implemented finding of initial ups

2010-01-21 13:21  twu

	* src/pairinggene.c: Initial import into CVS.  Dynamic programming
	  based on splicegene.c

2010-01-20 08:21  twu

	* src/spliceeval.c: Implemented computation of reception zone and
	  init/term status of splice sites

2010-01-20 06:21  twu

	* src/: gsnap.c, stage1hr.c, stage3hr.c, stage3hr.h: Implemented
	  trimming of ends of sequences

2010-01-20 01:30  twu

	* src/stage1hr.c: Allowing GC-AG splicing as well as GT-AG.  Using
	  a sliding scale of splice site probabilities based on alignment
	  support.

2010-01-20 01:29  twu

	* src/: stage3hr.c, stage3hr.h: Added code for using a geneprob IIT
	  file to assist in finding splice sites

2010-01-20 01:27  twu

	* src/gsnap.c: Added a -g flag for using a geneprob IIT file to
	  assist in finding splice sites

2010-01-19 10:38  twu

	* src/: tally.c, tally.h: Added function Tally_mean()

2010-01-19 10:37  twu

	* src/tallyflats.c: Analyzing both fwd and rev tallies and storing
	  in a single IIT file

2010-01-19 10:36  twu

	* src/splicegene.c: Using variability in pairing.unk rather than
	  tallyflats to determine intragenic regions

2010-01-19 10:35  twu

	* src/spliceeval.c: Computing slopes internally, rather than
	  relying upon pairingflats

2010-01-19 10:34  twu

	* src/pairingflats.c: Added median smoothing

2010-01-19 10:33  twu

	* src/: lgamma.c, lgamma.h: Added ppois function

2010-01-19 07:07  twu

	* src/genecompare.c: Initial import into CVS

2010-01-19 07:04  twu

	* src/geneeval.c: Changed name to genecompare.c

2010-01-19 07:01  twu

	* src/geneeval.c: Added ability to handle comment lines in gene

2010-01-17 08:21  twu

	* src/: lgamma.c, lgamma.h, random.c, random.h: Initial import into
	  CVS

2010-01-17 08:20  twu

	* src/: tally.c, tally.h: Added functions

2010-01-17 08:18  twu

	* src/geneeval.c: Printing goldstandard information in comment line

2010-01-17 08:17  twu

	* src/cappaths.c: Using pairing fwd and rev iits

2010-01-17 08:16  twu

	* src/spliceeval.c: Removed unused code.  Added procedures for
	  merging pairingflats.

2010-01-17 08:15  twu

	* src/splicegene.c: Added a check for validity tally flats by
	  looking at tally information

2010-01-17 08:14  twu

	* src/tallyflats.c: Keeping track separately of zero regions and
	  flat regions.  Changed parameters.

2010-01-17 08:13  twu

	* src/gsnap_splices.c: Removed unused code

2010-01-17 08:12  twu

	* src/gsnap_tally.c: Added flags for picking specific strands and
	  for forced trimming at ends

2010-01-17 08:11  twu

	* src/pairingstrand.c: Initial import into CVS

2010-01-17 08:10  twu

	* src/pairingflats.c: Storing regions and then printing them.  Have
	  three states, for zero, flat, and bumpy.

2010-01-17 08:09  twu

	* src/pairingcum.c: Print all run lengths, even those with level 0

2010-01-17 04:52  twu

	* src/splicegene.c: Using tallyflats to determine boundaries for
	  donor to acceptor

2010-01-17 03:26  twu

	* src/splicegene.c: Removed donorprob and acceptorprob.  Recording
	  and printing all extra information from each splice.	Removed
	  unused paths code.

2010-01-17 01:51  twu

	* src/tallyflats.c: Initial import into CVS

2010-01-16 10:29  twu

	* src/pairingflats.c: Initial import into CVS

2010-01-16 02:43  twu

	* src/spliceeval.c: Added a intron_transition buffer at the ends of
	  each intron, where level changes are ignored.

2010-01-15 09:01  twu

	* src/splicegene.c: Using a gap test on pairing IITs to determine
	  whether to link donor to previous acceptor.

2010-01-15 08:59  twu

	* src/spliceeval.c: Now computing statistics based on edge finding
	  using Poisson model and number of consecutive zeroes.

2010-01-15 01:27  twu

	* src/spliceeval.c: Printing mean pairing levels of each splice

2010-01-12 22:33  twu

	* src/tallyhmm.c: Integrated parserange and tally modules.  Removed
	  hints.  Added edge detection.  Simplified state model.

2010-01-12 09:52  twu

	* src/: tally.c, tally.h: Implemented an exon test and a scanning
	  solution for pairing information.

2010-01-12 09:50  twu

	* src/splicegene.c: Using an exon test to determine if we can join
	  splices

2010-01-12 06:51  twu

	* src/littleendian.c: Initial import into CVS

2010-01-12 06:49  twu

	* src/bigendian.c: Created distinct function names for 64-bit
	  procedures.  Added procedures for OUTPUT_BIGENDIAN.  Fixed
	  compiler warning messages about truncating unsigned ints to
	  chars.

2010-01-12 06:48  twu

	* src/bigendian.h: Created distinct function names for 64-bit
	  procedures

2010-01-11 22:26  twu

	* src/geneeval.c: Initial import into CVS

2010-01-11 08:28  twu

	* src/cappaths.c: Initial import into CVS

2010-01-09 07:54  twu

	* src/: tally.c, tally.h: Initial import into CVS

2010-01-08 08:59  twu

	* src/pairingcum.c: Initial import into CVS

2010-01-07 04:59  twu

	* src/splicegene.c: Computing exonbounds for each donor

2010-01-05 07:55  twu

	* src/tallyhmm.c: Using edges rather than edgepairs

2010-01-04 08:30  twu

	* src/: parserange.c, parserange.h, spliceeval.c: Initial import
	  into CVS

2010-01-04 08:06  twu

	* src/splicegene.c: Added iterative method to remove conflicting
	  splices

2010-01-04 01:05  twu

	* src/splicegene.c: Computing one path over forward and one path
	  over reverse strands, instead of collecting terminals

2010-01-03 07:15  twu

	* src/splicegene.c: Added reading and printing of probability
	  values.  Added debugging statements for Paths_remove_dominated

2009-12-28 11:27  twu

	* src/: stage1hr.c, stage1hr.h: Added separate stage for half
	  introns.  Added hook for geneprob_iit eval.

2009-12-22 03:41  twu

	* src/splicegene.c: Initial import into CVS

2009-12-22 01:22  twu

	* src/gsnap_splices.c: Added command for dumping graph

2009-12-21 08:45  twu

	* src/stage3hr.c: Added ability to print output in SAM format.
	  Fixed bug in identifying pairing.

2009-12-21 08:42  twu

	* src/: gsnap.c, stage3hr.h: Added ability to print output in SAM
	  format

2009-12-17 06:04  twu

	* src/exonscan.c: Added function for writing edges

2009-12-10 04:58  twu

	* src/stage1hr.c: Fixed bug in insertion at end of query sequence.
	  Removed requirement for HALF_INTRON_END_LENGTH.  Made separate
	  done levels for 5' and 3' ends in paired alignment.

2009-12-04 03:47  twu

	* src/gsnap_tally.c: Added ability to run on forward or reverse
	  complement strand only

2009-12-04 03:38  twu

	* src/gsnap_tally.c: Added ability to run on all chromosomes

2009-11-25 02:35  twu

	* src/stage1hr.h: Added new masktypes

2009-11-25 02:35  twu

	* src/stage1hr.c: Created a single procedure for omit_oligos.
	  Altered xfirst and xlast calculation.

2009-11-20 08:28  twu

	* src/stage1hr.c: Made slight efficiency improvements in accessing
	  floor->score array

2009-11-18 05:42  twu

	* src/stage2.c: Combined features of versions 235 and 237 for both
	  GMAP and PMAP to work.

2009-11-18 03:03  twu

	* src/stage2.h: Updated interface

2009-11-18 03:03  twu

	* src/stage2.c: Fixed bug where processed was updated too soon

2009-11-18 02:41  twu

	* src/: pairpool.c, pairpool.h: Added function Pairpool_transfer_n

2009-11-18 02:41  twu

	* src/orderstat.c: Commented out debugging function

2009-11-18 02:40  twu

	* src/: gmap.c, oligoindex.c: Restored variables specific to gmap

2009-11-18 02:29  twu

	* src/: oligoindex.c, oligoindex.h: Added major and minor
	  oligoindices

2009-11-18 02:28  twu

	* src/gmap.c: Added Oligoindex_clear_inquery in all cases

2009-11-18 01:54  twu

	* src/stage2.c: Restored stage 2 to working condition

2009-11-06 06:29  twu

	* src/: maxent.c, maxent.h: Added functions for reporting log odds
	  scores

2009-11-06 06:28  twu

	* src/littleendian.h: Added interface for WRITE_UINT

2009-11-06 06:28  twu

	* src/list.c: Added check for NULL in List_truncate

2009-11-06 06:27  twu

	* src/iit_fetch.c: Added flag for computing cumulative total of an
	  iit.	Removed unused variables.

2009-11-06 06:26  twu

	* src/iit_get.c: Added flags for computing mean and overall total
	  of tally iit.

2009-11-04 07:59  twu

	* src/add_rpk.c: Initial import into CVS

2009-10-30 07:38  twu

	* src/: exonscan.c, hint.c, hint.h, tallyhmm.c: Using edgepair and
	  splice information in transitions, and tally and pairing
	  information in emissions.  Providing separate training
	  information for transitions and emissions.

2009-10-27 04:01  twu

	* src/: hint.c, hint.h: Initial import into CVS

2009-10-26 06:21  twu

	* src/stage3.c: Removed unused variables

2009-10-14 05:13  twu

	* src/pair.c: Fixed bug in PSL output

2009-10-08 05:31  twu

	* src/: exonscan.c, tallyhmm.c: Multiple changes.  Version used for
	  rGASP submission 2.

2009-10-02 10:04  twu

	* src/: stage3hr.c, stage3hr.h: Made printing of score and insert
	  length more consistent.  Made filtering of paired hits by score
	  and duplicates consistent with filtering of single hits.

2009-10-02 10:02  twu

	* src/: resulthr.c, resulthr.h: Removed Pairedresult_T type

2009-10-02 10:02  twu

	* src/: gsnap.c, stage1hr.c, stage1hr.h: Allowing user to specify
	  max mismatches as a fraction of read length

2009-10-02 08:30  twu

	* src/stage3hr.c: Made printing of insert length consistent for
	  paired-end reads

2009-10-02 06:44  twu

	* src/: stage1hr.c, stage1hr.h, gsnap.c: Added parameters for
	  minimum end matches for local and distant splicing

2009-10-01 10:58  twu

	* src/spanningelt.c: Made intersection procedures remove duplicates

2009-10-01 10:56  twu

	* src/snpindex.c: Formatting change

2009-10-01 10:55  twu

	* src/gsnap.c: Added parameters for second part of novel splicing
	  and half intron minimum support

2009-10-01 10:54  twu

	* src/: genome_hr.c, genome_hr.h: Returning ncolordiffs

2009-10-01 10:53  twu

	* src/gbuffer.h: Added procedures for allocing and freeing contents

2009-10-01 10:53  twu

	* src/blackboard.c: Fixed problem with hanging when using -q batch
	  feature

2009-10-01 10:52  twu

	* src/stage1hr.c: Made min_end_matches work on middle indels

2009-10-01 10:51  twu

	* src/stage3hr.h: Added printing of colordiffs and score.

2009-10-01 10:51  twu

	* src/stage3hr.c: Added printing of colordiffs and score.  Fixed
	  problem with printing splice on second, inverted read.

2009-10-01 03:37  twu

	* src/stage1hr.h: Added half_intron_min_support parameter.

2009-10-01 03:36  twu

	* src/stage1hr.c: Added half_intron_min_support parameter.  Fixed
	  bug where deletion indels were mixed up with colordiffs.  Fixed
	  bug where splice junctions were evaluated past beginning of
	  genome.

2009-09-21 12:38  twu

	* src/tallyhmm.c: Uses hints from splices iit and altexons iit
	  files.  Added median filtering.

2009-09-21 09:21  twu

	* src/exonscan.c: Added ability to get splice sites from splices
	  iit and altexons iit file

2009-09-21 02:56  twu

	* src/tallyhmm.c: Adding information from splices_iit and
	  altexons_iit files

2009-09-20 22:35  twu

	* src/tallyhmm.c: Implemented two-strand solution as default, with
	  ability to force 1-strand solution.  Provided hooks for splices
	  and altexons iit files.

2009-09-20 20:00  twu

	* src/gsnap_tally.c: Added flag for handling 2-base encoded GSNAP
	  output

2009-09-20 19:59  twu

	* src/gsnap_splices.c: Eliminated printing of overlapping paths.

2009-09-20 10:50  twu

	* src/gsnap_splices.c: Fixed various bugs

2009-09-20 09:04  twu

	* src/gsnap_splices.c: Added ability to find alternate skipped or
	  extra exons at each acceptor.

2009-09-20 06:27  twu

	* src/gsnap_splices.c: Initial import into CVS

2009-09-19 14:34  twu

	* src/tallyhmm.c: Implemented faster way of computing running
	  percentiles

2009-09-19 11:37  twu

	* src/tallyhmm.c: Implemented ability to read lambda parameters
	  from a file.	Attempted to add a SINGLE exon state and allow
	  transitions from NON to SINGLE even when no edges were present.

2009-09-19 10:09  twu

	* src/gsnap_tally.c: Had program determine own trimming based on
	  scoring matches and mismatches from the ends.

2009-09-19 09:28  twu

	* src/iit_get.c: Added -M flag for reporting mean of a region in a
	  tally IIT file.

2009-09-19 00:21  twu

	* util/gsnap_splicing.pl: Initial import into CVS

2009-09-18 12:49  twu

	* src/exonscan.c: Printing information about sharp edges

2009-09-18 04:45  twu

	* src/exonscan.c: Fixed bug in recording history.  Added hook for
	  allowing GC donor site.  Added splice model probability to name
	  of splice site.

2009-09-18 03:03  twu

	* src/tallyhmm.c: Added flag for printing lambdas

2009-09-17 17:56  twu

	* src/tallyhmm.c: Added ability to handle multiple sites at the
	  same position, by making a mixture of transition tables.  Wrote
	  down transition table explicitly.

2009-09-17 16:35  twu

	* src/tallyhmm.c: Added smoothing to estimation of lambdas.  Added
	  routines for printing genes.

2009-09-17 10:49  twu

	* src/tallyhmm.c: Consolidated separate fivefwd, fiverev, threefwd,
	  and threerev sites back into up and down sites.

2009-09-17 10:23  twu

	* src/tallyhmm.c: Working version of Viterbi algorithm, but still
	  need output of segments.

2009-09-17 07:06  twu

	* src/tallyhmm.c: Initial import into CVS

2009-09-17 00:22  twu

	* src/segue.c: Attempt to use objective function based on sum of
	  counts, relative to threshold.

2009-09-16 17:12  twu

	* src/segue.c: Reduced states to be much simpler, where only one
	  strand can be coding at a time.

2009-09-16 16:03  twu

	* src/segue.c: Added functions for printing genes by exons.

2009-09-16 13:52  twu

	* src/segue.c: Fixed lookback lengths between sites.  Added flag
	  for specifying knownsites iit.

2009-09-16 07:49  twu

	* src/segue.c: Optimizing using mean square error.  Simplified code
	  for traversing graph.

2009-09-16 04:52  twu

	* src/segue.c: Fixed bug with computing cumulative gammln.  Version
	  works on test data set.

2009-09-16 02:57  twu

	* src/segue.c: Complete rewrite to handle both strands
	  simultaneously

2009-09-15 08:18  twu

	* src/exonscan.c: Using LR test to take all acceptable gene ends.
	  Using separate end bounds for finding gene ends.

2009-09-15 06:58  twu

	* src/exonscan.c: Using both edge algorithms, stepfunction and
	  linear fit.  Made different objects for Edge_T and Diff_T.  Using
	  goodness-of-fit instead of xintercept for finding gene ends.

2009-09-14 18:33  twu

	* src/exonscan.c: No longer using bootstrap method, but relying on
	  testing of sites using goodness of fit.  Evaluating missing edges
	  for both ups and downs based only on greedy splice sites, and
	  then performing both testing of sites and tracing.

2009-09-14 16:31  twu

	* src/exonscan.c: Using x-intercepts instead of step function to
	  detect edges

2009-09-14 11:21  twu

	* src/exonscan.c: Added hooks for a history-recording mechanism.

2009-09-14 09:26  twu

	* src/exonscan.c: Fixed some bugs with array indices.  Added flags
	  for debugging.

2009-09-14 05:42  twu

	* src/segue.c: Using splice model scores to evaluate introns

2009-09-13 16:07  twu

	* src/exonscan.c: Made numerous tweaks to the scanning algorithm.
	  Incorporated finding of ends into scanning, using x-intercepts.
	  Always finding ends when an edge with a splice lacks a match.

2009-09-13 09:30  twu

	* src/exonscan.c: Implemented two-phase method on stepfunction
	  results, first picking steps with highest probabilities, and then
	  bootstrapping neighboring steps.

2009-09-13 07:43  twu

	* src/exonscan.c: Allowed best prob again for stepfunction results.
	  Fixed bug in code in scanning procedure.  Distinguishing between
	  donor and acceptor types for matching edges.

2009-09-13 02:22  twu

	* src/exonscan.c: Large numbers of changes.  Implemented scanning
	  method, testing at positions with good splice site scores, for
	  finding other ends.  Using adjacency information to decide
	  whether to scan.  Implemented testing procedures for ends.
	  Removed unused code.

2009-09-12 16:56  twu

	* src/exonscan.c: Implemented a Gibbs sampling method to speed up
	  identification of changepoint, but reverted back to testing
	  goodness of fit exhaustively over a limited range.

2009-09-12 12:14  twu

	* src/exonscan.c: Implemented a strategy of finding edges only for
	  those that appear to be missing.  Using changepoint to find those
	  edges, with maximizing goodness of fit.

2009-09-12 03:18  twu

	* src/exonscan.c: Made reasonably good step function based on log
	  scale.

2009-09-12 01:00  twu

	* src/exonscan.c: Implemented rampfunction as anchored to a step
	  result.

2009-09-11 12:23  twu

	* src/exonscan.c: Implemented a ramp detector using linear fitting,
	  but too sensitive

2009-09-11 04:27  twu

	* src/exonscan.c: Using a cumulative tally to speed up computation
	  of segment means

2009-09-11 04:08  twu

	* src/exonscan.c: Added hooks for a redo changepoint step

2009-09-11 02:19  twu

	* src/segue.c: Implemented traversal of minus strand.  Implemented
	  reading of splicepairs.

2009-09-10 23:13  twu

	* src/segue.c: Implemented scoring of exons using log likelihood.
	  Implemented dynamic programming and printing of paths.

2009-09-10 15:29  twu

	* src/exonscan.c: Added splice sites based on analyzing local data,
	  using methodology from splicescan.

2009-09-10 08:37  twu

	* src/splicescan.c: Implemented posterior log odds calculations.

2009-09-10 08:36  twu

	* src/exonscan.c: Added filtering of other ends.  Cleaned up unused
	  code.

2009-09-10 02:59  twu

	* src/exonscan.c: Made output format consistent with that of
	  splicescan

2009-09-10 01:01  twu

	* src/segue.c: Initial import into CVS

2009-09-10 00:59  twu

	* src/exonscan.c: Added finding of nearest good splice sites.

2009-09-09 13:57  twu

	* src/exonscan.c: Method based on finding exons.  However, will
	  need to switch to a dynamic programming method.

2009-09-09 13:14  twu

	* src/exonscan.c: Initial import into CVS

2009-09-08 15:13  twu

	* src/splicescan.c: Added options for separate output files,
	  training mode only, and random output.

2009-09-07 23:05  twu

	* src/stage1hr.c: Fixed algorithm for end indels.  Provided hooks
	  for 2-base encoding.

2009-09-07 15:11  twu

	* src/splicescan.c: Fixed calculations

2009-09-06 15:40  twu

	* src/splicescan.c: Added ability to use a known splice site IIT
	  file

2009-09-06 04:00  twu

	* src/splicescan.c: Initial import into CVS

2009-09-03 09:05  twu

	* src/stage1hr.c: Fixed bug where singlehits5 and singlehits3 not
	  being initialized.  Set limits on local splicing hits and
	  attempts.

2009-09-02 03:45  twu

	* src/: stage3.c, stage3.h: Allowing a re-do of stage 2 for bad
	  exons in middle

2009-08-31 01:57  twu

	* src/gsnap.c: Using single-end hits already computed when paired
	  alignments not found.

2009-08-31 01:56  twu

	* src/gmap.c: Added minor oligoindices

2009-08-31 01:56  twu

	* src/changepoint.c: Added comment

2009-08-31 01:55  twu

	* src/: stage3hr.c, stage3hr.h: Introduced faster pair-up
	  procedure.  Sorting paired-end solutions by score.

2009-08-31 01:54  twu

	* src/stage1hr.h: For paired-end alignment, returning single-end
	  hits.

2009-08-31 01:54  twu

	* src/stage1hr.c: Fixes to paired-end alignment: (1) stopping when
	  excessive splicing hits or paired hits found, (2) using new
	  pair_up procedure, (3) fixed pairing code, (4) returning
	  single-end hits.  For dibase alignment, skipping spanning set.

2009-08-31 01:51  twu

	* src/iit_store.c: Using total label and annotation lengths to
	  decide if format should use 8-byte quantities.

2009-08-31 01:50  twu

	* src/iit_get.c: Added flag to explicitly indicate coordinate is a
	  label.  Added flag to print all zeroes in tally mode.

2009-08-28 10:47  twu

	* src/: stage3hr.c, stage3hr.h: Taking a splicing penalty for all
	  splices.  Added code for marking dibase mismatches.

2009-08-28 10:43  twu

	* src/: stage1hr.c, stage1hr.h: Made procedure work for 2-base
	  encoded reads

2009-08-28 10:38  twu

	* src/oligo.c: Added code to read 2-base encoded queries

2009-08-28 10:37  twu

	* src/: reader.c, reader.h: Added field to indicate if Reader_T is
	  for dibase queries

2009-08-28 10:36  twu

	* src/littleendian.h: Added code for handling 8-byte quantities

2009-08-28 10:36  twu

	* src/: iit-read.c, iit-write.c, iitdef.h: Added version 4 format,
	  which uses 8-byte quantities to store label pointers and
	  annotation pointers.

2009-08-28 10:33  twu

	* src/gsnap_tally.c: Added trimming on left and right

2009-08-28 10:33  twu

	* src/gsnap.c: Added flag for 2-base mode.  Added local splice
	  penalty.

2009-08-28 10:32  twu

	* src/: genome_hr.c, genome_hr.h: Provided hooks for dibase
	  procedures

2009-08-28 10:31  twu

	* src/: genome.c, genome.h: Provided exposure to uncompress_mmap
	  directly from blocks, needed by dibase procedures.

2009-08-28 10:28  twu

	* src/: dibase.c, dibase.h: Initial import into CVS

2009-08-28 10:28  twu

	* src/compress.c: Added code for compressing 2-base color genomes,
	  but not necessary.

2009-08-28 10:27  twu

	* src/: bigendian.c, bigendian.h: Added functions for 8-byte
	  quantities

2009-08-28 10:27  twu

	* src/access.c: Changed types in debugging statements for off_t

2009-08-21 05:41  twu

	* src/oligo.c: If state is invalid, skipping forward until a valid
	  state is found

2009-08-21 05:26  twu

	* src/sequence.h: Added FILE * parameter for oneline outputs.

2009-08-21 05:26  twu

	* src/sequence.c: Added FILE * parameter for oneline outputs.
	  Added hooks for skipping dashes, but appears to be buggy.

2009-08-21 05:21  twu

	* src/gsnap.c: Added flag to turn off output (quiet) if too many
	  are found.

2009-08-21 05:20  twu

	* src/stage1hr.c: Classified half introns as long distance

2009-08-20 10:48  twu

	* src/stage1hr.c: Moved half introns after distant splicing.  Set
	  fast_level to be 1, if user hasn't already specified it.

2009-08-19 04:24  twu

	* util/gmap_setup.pl.in: Using "use warnings" instead of -w flag

2009-08-18 15:13  twu

	* src/stage3hr.h: Added quiet-if-excessive flag.

2009-08-18 15:12  twu

	* src/stage3hr.c: Fixed problem where total_nmismatches not being
	  set for indels.  Making printing of excessive paths consistent
	  with single-end behavior.

2009-08-18 15:11  twu

	* src/stage1hr.c: Fixed problem where pair_up function was creating
	  circular loops by calling List_append more than once.

2009-08-18 15:10  twu

	* src/: list.c, list.h: Added function List_dump

2009-08-17 06:35  twu

	* src/: gsnap-to-iit.c, gsnap_tally.c: Renamed gsnap-to-iit.c to
	  gsnap_tally.c

2009-08-17 05:49  twu

	* src/stage1hr.c: Fixed bug where program tried to find deletions
	  at end extending past coordinate 0U.

2009-08-14 02:57  twu

	* src/stage3hr.c: Revised paired-end output to show npaths and
	  indication of paired or unpaired.

2009-08-14 02:35  twu

	* src/: gsnap.c, bigendian.c, mem.c: Fixed compiler warnings from
	  -Wall

2009-08-14 02:01  twu

	* src/iit-read.c: Fixed compiler warnings from -Wall

2009-08-14 01:53  twu

	* src/iit-read.c: Fixed bug where divno not checking the last div.

2009-08-14 01:52  twu

	* src/sequence.h: Added a function to the interface

2009-08-14 01:52  twu

	* src/sequence.c: Fixed compiler warnings from -Wall

2009-08-14 01:33  twu

	* src/genome.c: Fixed compiler warnings from -Wall

2009-08-14 01:32  twu

	* src/genome.c: Using SNP_FLAGS for getting alternate genome

2009-08-14 01:27  twu

	* src/indexdb.c: Fixed compiler warnings from -Wall

2009-08-14 01:05  twu

	* src/: indexdb.c, indexdb.h: Added procedure for reading with
	  diagterm and sizelimit

2009-08-14 00:56  twu

	* src/indexdb_hr.c: Fixed compiler warnings from -Wall

2009-08-14 00:51  twu

	* src/indexdb_hr.c: Providing information about nmerged

2009-08-14 00:49  twu

	* src/maxent.h: Defined a variable to specify maximum storage
	  required

2009-08-14 00:48  twu

	* src/maxent.c: Added code for computing splices from revcomp
	  sequences

2009-08-14 00:46  twu

	* src/cmet.c: Added a missing type

2009-08-14 00:44  twu

	* src/stage3hr.c: Fixed compiler warnings from -Wall.

2009-08-14 00:41  twu

	* src/genome_hr.c: Fixed compiler warnings from -Wall.

2009-08-14 00:40  twu

	* src/stage1hr.h: Added Floors_free() to interface.

2009-08-14 00:40  twu

	* src/stage1hr.c: Fixed bug where unsigned int * assigned to signed
	  int *.  Fixed compiler warnings from -Wall.

2009-08-04 06:45  twu

	* src/: list.c, list.h: Added function List_truncate

2009-08-04 06:44  twu

	* src/: pair.c, pair.h: Added function Pair_fracidentity_max

2009-08-04 06:44  twu

	* src/stage3.h: Added some interfaces

2009-08-04 06:43  twu

	* src/stage3.c: Forward/reverse decision based on local scoring
	  around each intron.  Distal/medial step now truncates distal exon
	  at best point, and iterates.	When edges cross in changepoint
	  step, now chopping shortest end.

2009-08-04 06:40  twu

	* src/stage2.c: Allowing rightward and leftward shifts in finding
	  shifted canonical introns.  Fixed bug in scoring for reverse
	  introns.  Adjusted scoring for canonical introns.

2009-08-04 06:37  twu

	* src/stage1.h: Imposing a size limit on position lists, so large
	  ones are ignored.

2009-08-04 06:37  twu

	* src/stage1.c: Imposing a size limit on position lists, so large
	  ones are ignored.  Finding best solutions for each level of
	  numbers of exons.

2009-07-30 08:55  twu

	* src/stage3.c: Using existing pairs/path in end exons, rather than
	  recomputing in distal/medial calculation.  Moved distal/medial
	  after changepoint.

2009-07-30 08:54  twu

	* src/stage3.h: Moved distal/medial calculation to be after
	  changepoint

2009-07-30 02:29  twu

	* README: Added information about processing reads from
	  bisulfite-treated DNA

2009-07-30 01:45  twu

	* src/stage1hr.c: Making correct decision on when to find splice
	  ends for half introns

2009-07-30 01:43  twu

	* src/: gsnap.c, stage3hr.c, stage3hr.h: Added printing of SNP
	  information

2009-07-30 01:43  twu

	* src/gmap.c: Added indexdb_size_threshold.  Made -9 flag do
	  checking, but not print full diagnostics.

2009-07-30 01:42  twu

	* src/dynprog.c: Made gap penalties at ends the same as for middle

2009-07-30 01:41  twu

	* src/diag.c: Added debugging statement

2009-07-30 01:41  twu

	* src/Makefile.gsnaptoo.am: Included snpindex

2009-07-29 09:40  twu

	* README: Added information about providing information to GSNAP
	  about known splice sites and SNPs

2009-07-29 06:44  twu

	* src/gsnap.c: Increased default max_middle_insertions from 6 to 9

2009-07-29 06:41  twu

	* src/stage1hr.c: Checking entire query for nsnpdiffs when
	  snp_blocks is present

2009-07-06 23:48  twu

	* src/stage1.c: In find_best_path, calculating median of segments
	  and requiring that medians ascend or descend.  Adjusting scores
	  for overlaps between segments.

2009-07-01 05:32  twu

	* src/: stage1hr.c, stage1hr.h, gsnap.c: Added separate probability
	  thresholds for local and distant splicing

2009-07-01 00:45  twu

	* src/: stage1hr.c, stage1hr.h: Re-implemented paired-end alignment

2009-06-29 11:00  twu

	* src/: gsnap.c, stage1hr.c, stage1hr.h, stage3hr.c, stage3hr.h:
	  Introduced a penalty for distant splicing

2009-06-29 10:35  twu

	* src/gsnap.c: Introduced masktype

2009-06-29 10:34  twu

	* src/: stage3hr.c, stage3hr.h: Introduced chimera_prob field for
	  Stage3_T object.  Increased distantsplicing penalty from 1 to 2.

2009-06-29 07:30  twu

	* src/stage1hr.c: For novel splice sites in local splicing,
	  requiring canonical dinucleotides plus sufficient probability
	  score in either donor or acceptor.  Fixed bug in recognizing plus
	  antisense splicing.  Restricted half introns to known splice
	  sites.

2009-06-29 01:12  twu

	* src/stage1hr.h: Added masktype

2009-06-29 01:11  twu

	* src/stage1hr.c: Added masktype.  Added back half introns.

2009-06-28 10:45  twu

	* src/stage1hr.c: Merged finding of distant splice pairs using
	  known or novel splice sites.

2009-06-28 01:11  twu

	* src/stage1hr.c: Consolidated finding of splice pairs using known
	  or novel splice sites.  Making a single call to retrieve genomic
	  segment for local splicing.

2009-06-26 06:55  twu

	* src/stage1hr.c: Removed unused tournament and middle_indel_p code

2009-06-26 05:34  twu

	* src/stage1hr.c: Using floors for novel distant splicing

2009-06-26 02:11  twu

	* src/stage1hr.c: Using floors for finding novel local splicing

2009-06-26 01:16  twu

	* src/stage3hr.h: Added field for paired_up

2009-06-26 01:16  twu

	* src/stage3hr.c: Added field for paired_up.  Removing duplicates
	  that differ in indel gap length.

2009-06-25 09:29  twu

	* src/stage1hr.h: Implemented paired-end alignment

2009-06-25 09:29  twu

	* src/stage1hr.c: Implemented paired-end alignment.  Fixed
	  computation of floors for middle indels.  Fixed computation of
	  find_segments_all for novel splicing.

2009-06-18 09:05  twu

	* src/: Makefile.dna.am, Makefile.gsnaptoo.am: Removed segmentpool
	  files from Makefile.am

2009-06-18 09:05  twu

	* src/: gsnap.c, segmentpool.c, segmentpool.h, stage1hr.c,
	  stage1hr.h: Removed all references to segmentpool

2009-06-18 08:58  twu

	* src/stage1hr.c: Removed code for Segmentpool_T

2009-06-18 08:57  twu

	* src/: segmentpool.c, segmentpool.h: Removed some fields

2009-06-18 07:10  twu

	* src/stage1hr.c: Fixed bug resulting from resetting
	  nmismatches_all unnecessarily

2009-06-18 07:10  twu

	* src/stage3.c: Fixed bug in computing goodness_rev

2009-06-09 05:50  twu

	* src/dynprog.c: Increased penalties for mismatch at ends and for
	  opening indels around introns.

2009-06-09 05:50  twu

	* src/gsnap.c: Increased default definition of shortsplicedist from
	  200000 to 500000.

2009-06-09 05:49  twu

	* src/stage1hr.c: Fixed bugs in dealing with empty plus_segments or
	  minus_segments.

2009-06-08 01:54  twu

	* src/stage1hr.c: Created variables for faster retrieval of floor
	  scores.  Reporting half introns only if both local and distant
	  known splicing fail.

2009-06-07 16:03  twu

	* src/stage1hr.c: Fixed computation of floors, floor_xfirst, and
	  floor_xlast

2009-06-07 04:35  twu

	* src/stage1.c: Fixed bug in debugging variables

2009-06-07 04:34  twu

	* src/stage1hr.c: Implemented code that does not use Segmentpool_T
	  object

2009-06-07 04:34  twu

	* src/pair.c: Treating ambiguous characters as mismatches for
	  computing matchscores

2009-06-07 04:33  twu

	* src/gmap.c: Proving an option for splicesites output.  Allowing
	  use of a SNP genome version.

2009-06-07 04:32  twu

	* src/dynprog.c: Giving ambiguous characters a negative score in
	  GMAP, but not PMAP

2009-06-07 04:31  twu

	* src/stage3.c: Computing direction using just canonical introns
	  and indel openings

2009-06-07 01:02  twu

	* src/stage1hr.c: Removed middle_indel_p field in Segment_T object

2009-06-06 09:04  twu

	* src/: segmentpool.c, segmentpool.h, stage1hr.c: Removed floor
	  from the Segmentpool_T object

2009-06-06 09:01  twu

	* src/: segmentpool.c, segmentpool.h: Added a procedure for pushing
	  without any floors

2009-06-06 09:00  twu

	* src/stage3hr.c: Added a penalty for distant splicing

2009-06-06 08:58  twu

	* src/stage1hr.c: Performing local and distant splicing in separate
	  levels

2009-06-05 02:47  twu

	* src/: stage3.h, pair.c, pair.h: Added a function for printing
	  splicesites

2009-06-05 02:47  twu

	* src/stage3.c: Reinstated checking of goodness to determine
	  direction, but now considering just canonical introns and indels.
	  Added a final call to assign_gap_types after trimming.

2009-06-04 12:31  twu

	* src/stage1hr.c: Small improvements to code for binary_search and
	  dual_search

2009-06-04 03:43  twu

	* src/stage1hr.c: Made improvements in code for dual_search by
	  removing lowi and lowj and updating pointers for positions1 and
	  positions2.

2009-06-03 13:36  twu

	* src/stage1hr.c: Using single splicesites list for novel local
	  splicing

2009-06-03 12:52  twu

	* src/stage1hr.c: Implemented slightly more efficient code for
	  dual_search.

2009-06-03 11:59  twu

	* src/: stage1hr.c, stage1hr.h, gsnap.c: Improved speed of finding
	  known splicesites by doing one dual_search for all splice types.

2009-06-03 01:36  twu

	* src/stage1hr.c: Revised dual_search procedure to handle
	  overlapping splicesites and positions correctly.

2009-06-02 14:27  twu

	* src/genome_hr.c: Fixed bug in handling pos5 for
	  Genome_mismatches_left.

2009-06-02 14:18  twu

	* src/stage1hr.c: Fixed dual_search so it handles all overlapping
	  splicesites and intervals

2009-06-02 02:25  twu

	* src/stage1hr.c: Implemented faster code for finding novel splice
	  ends

2009-06-02 01:22  twu

	* src/stage1hr.c: Changed Floors_T to be just a single set of
	  scores.  Using floors to prune known splice ends.

2009-06-01 05:19  twu

	* src/stage3hr.c: Removed genomiclength from Stage3_T object.
	  Using chrnum of 0 to indicate distant splicing.

2009-06-01 05:19  twu

	* src/stage1hr.c: Removed oldindels code

2009-05-29 10:53  twu

	* src/stage1hr.c: Using compressed nucleotide-level alignment for
	  end indels.  Preventing firstbound and lastbound from going past
	  read boundaries.

2009-05-29 05:15  twu

	* src/stage1hr.c: Fixed assignment of shortdistancep in splice
	  pairs.  Fixed assignments of prior penalties.

2009-05-25 00:21  twu

	* src/stage3hr.c: Eliminating duplicates where genomicstart and
	  genomicend are equal

2009-05-25 00:21  twu

	* src/stage1hr.c: Excluding splice positions at ends in novel local
	  splicing

2009-05-25 00:18  twu

	* src/genome_hr.c: Fixed bug in mismatches_right_snps where
	  startdiscard was not being applied

2009-05-24 13:54  twu

	* src/stage3hr.h: Added genomicend to Stage3_T object

2009-05-24 13:54  twu

	* src/stage3hr.c: Made removal of duplicates work for splicing by
	  adding genomicend to Stage3_T object.  Made removal of duplicate
	  splice ends faster.

2009-05-24 13:53  twu

	* src/stage1hr.c: Eliminating splice ends where splice position
	  occurs too close to the beginning.  Fixed triage to treat novel
	  splicing and known splicing equally, and to give preferences to
	  substitutions over indels over splicing when hits are found at
	  each type.

2009-05-24 01:44  twu

	* src/gsnap.c: Passing only one splice prob to stage 1

2009-05-24 01:44  twu

	* src/stage3hr.c: Lookin up splicesites iit only if site was known

2009-05-24 01:43  twu

	* src/stage1hr.h: Passing only one splice prob.

2009-05-24 01:43  twu

	* src/stage1hr.c: Implemented finding of novel distant splice
	  pairs.  Fixed bug in dual_search.

2009-05-22 18:10  twu

	* src/stage1hr.c: Implemented novel local splicing, which includes
	  known splice sites

2009-05-22 13:09  twu

	* src/: stage1hr.c, indexdb_hr.c, indexdb_hr.h, spanningelt.c:
	  Implemented gallop search

2009-05-22 09:39  twu

	* src/: stage1hr.c, stage1hr.h: Implemented a new flow through the
	  different algorithms.

2009-05-22 01:52  twu

	* src/gsnap.c: Made shortsplicedist an unsigned int.  Changed name
	  of spliceprob to minspliceprob.

2009-05-22 01:51  twu

	* src/stage3hr.c: Using total number of mismatches to score spliced
	  reads

2009-05-22 01:51  twu

	* src/stage1hr.c: Implemented dual intersection method for finding
	  known splice sites

2009-05-22 01:38  twu

	* src/: genome_hr.h, genome_hr.c: Added substring parameters to
	  Genome_count_mismatches_limit

2009-05-20 11:31  twu

	* src/stage1hr.h: Changed name from spliceprob to minspliceprob

2009-05-20 11:31  twu

	* src/stage1hr.c: Moved mismatches, indels, and splicing into a
	  single procedure.  Using firstbound and lastbound for half
	  introns.  Added provisions for a stretch procedure which uses a
	  spanning set with nrequired = 1.

2009-05-20 11:29  twu

	* src/stage2.c: Modified debugging output

2009-05-20 11:29  twu

	* src/oligoindex.c: Removed unnecessary clearing step

2009-05-20 11:28  twu

	* src/gmap.c: Fixed bug where program failed to clear oligoindices
	  after a poor or repetitive sequence.

2009-05-17 11:36  twu

	* src/: gsnap.c, genome_hr.c: Enabled methylation mode on snp
	  databases

2009-05-17 11:35  twu

	* src/indexdb.c: Improved pre-loading messages for snp databases

2009-05-17 11:35  twu

	* src/snpindex.c: Changed naming convention for snp databases

2009-05-17 11:34  twu

	* src/stage1hr.c: Fixed bug in calling new substitution with fixed
	  value for cmetp.

2009-05-17 11:32  twu

	* src/cmetindex.c: Made the program work for snp databases

2009-05-16 23:50  twu

	* src/: stage3hr.c, stage3hr.h: Stage3 now handles all marking of
	  mismatches.  Implemented marking of methylation for indels.

2009-05-16 23:49  twu

	* src/stage1hr.c: Moved functions for counting and marking
	  mismatches to stage3hr.c

2009-05-16 23:47  twu

	* src/gsnap.c: Removed call to specify methylation printing

2009-05-16 23:46  twu

	* src/: genome.h, genome.c: Removed function for signaling
	  methylation printing

2009-05-16 00:10  twu

	* src/stage1hr.h: Providing second indexdb and size_threshold to
	  procedures.

2009-05-16 00:10  twu

	* src/stage1hr.c: Omitting frequent 12-mers in the middle and
	  poly-AT 12-mers at the ends.	Performing another round without
	  omitting 12-mers if necessary.  Added first implementation for
	  handling methylation data.

2009-05-16 00:06  twu

	* src/: oligo.c, oligo.h: Changed definition of repetitive to mean
	  only shifts of 1, 2, or 3 nucleotides.  Added procedure to mark
	  frequent oligos, but not used.

2009-05-16 00:04  twu

	* src/: indexdb.c, indexdb.h: Added procedure to compute indexdb
	  mean size.

2009-05-16 00:04  twu

	* src/gsnap.c: Added flag to deal with methylation data.  Passing
	  size_threshold to stage 1 procedure.

2009-05-16 00:02  twu

	* src/: genome_hr.c, genome_hr.h: Added procedures to deal with
	  methylation data.

2009-05-16 00:01  twu

	* src/cmetindex.c: Creating two indexdb's, one for plus strand and
	  one for minus strand.  Moved conversion tables to cmet.c.
	  Removed conversion of genome.

2009-05-14 02:58  twu

	* src/: cmet.c, cmet.h: Initial import into CVS

2009-05-13 11:12  twu

	* src/cmetindex.c: Initial import into CVS.  Implements reverse
	  genome.

2009-05-13 08:08  twu

	* src/iit-read.c: Added warning for use of IIT_string_from_position

2009-05-13 08:08  twu

	* src/stage2.c: Fixed bug in using wrong indexsize for a given
	  oligoindex

2009-05-13 08:08  twu

	* src/: oligoindex.c, oligoindex.h: Added a procedure to return
	  indexsize

2009-05-13 08:05  twu

	* src/get-genome.c: Fixed printing of coordinates

2009-05-13 04:31  twu

	* src/: stage1hr.c, stage1hr.h: Changed polyat to omitted.  Created
	  separate procedure to mark omitted, which omits repetitive oligos
	  except at the ends, except for poly-AT at the ends.

2009-05-12 23:19  twu

	* src/: stage3hr.c, stage3hr.h: Made removal of duplicates faster

2009-05-12 23:18  twu

	* src/: stage1hr.c, stage1hr.h: Added ability to handle methylation
	  data.  Using simplified version of Genome_fill_buffer that does
	  not check chromosome bounds.

2009-05-12 23:17  twu

	* src/snpindex.c: Changed name of SNP genome file from genome to
	  genomecomp.

2009-05-12 23:16  twu

	* src/: genome.c, genome.h, gsnap.c: Added ability to handle
	  methylation data

2009-05-11 02:28  twu

	* src/gsnap.c: Made min_end_matches a user-adjustable parameter.
	  Made maxchimerapaths the same as maxpaths.

2009-05-11 02:28  twu

	* src/stage1hr.h: Made min_end_matches a user-adjustable parameter

2009-05-11 02:27  twu

	* src/stage1hr.c: Fixed computation of end indels so it finds
	  maximal length from end.  Made min_end_matches a user-adjustable
	  parameter.  Removed allocation of polyat outside of
	  0..query_lastpos.

2009-05-10 01:17  twu

	* src/stage1hr.c: Fixed bug in turning off end indels.	Implemented
	  faster method for computing firstbound and lastbound for xfirst
	  and xlast computation.

2009-05-07 22:58  twu

	* src/stage3hr.c: Fixed sorting so it uses hittype, and not indel
	  separation

2009-05-07 22:57  twu

	* src/: oligo.c, oligo.h: Added function Oligo_mark_repetitive

2009-05-07 22:56  twu

	* src/stage1hr.c: Fixed computations of xfirst and xlast in
	  presence of repetitive oligos.  Increased speed of computing
	  nmismatches_long in end indels.

2009-05-07 22:53  twu

	* src/: genome_hr.c, genome_hr.h: Modified Genome_mismatches_left
	  and Genome_mismatches_right to take pos5 and pos3 as arguments.

2009-05-07 11:03  twu

	* src/stage1hr.c: Fixed floor formulas again.  Generalized idea of
	  polyat to mean all repetitive oligos.  For middle indels,
	  computing middle floor explicitly when polyat oligos are present.
	  For end indels, computing firstbound and lastbound to handle
	  cases with polyat oligos at the ends.  Reordered
	  compute_end_indels to starting computing from 1 deletion.

2009-05-06 08:11  twu

	* src/: stage1hr.c, spanningelt.c, spanningelt.h: Removed unused
	  code

2009-05-06 07:56  twu

	* src/: spanningelt.c, spanningelt.h: Added code for spanning set
	  computation of end indels, but not used.

2009-05-06 07:55  twu

	* src/: stage1hr.h, gsnap.c: Added floors_array

2009-05-06 07:54  twu

	* src/stage1hr.c: Made changes to floors: (1) Made floor_middle
	  formula handle middle indels, (2) Created Floors_T object to
	  precompute floors and handle polyat oligomers.  Fixed computation
	  of end indels, now can handle mismatches.  Fixed bug in computing
	  max_indel_sep.  Added code for possible fast computation of end
	  indels, but not used.

2009-05-05 03:20  twu

	* src/stage1hr.c: Replaced arithmetic expression for smallesti with
	  if statement.

2009-05-05 03:13  twu

	* src/stage3hr.c: Changed sorting order so non-indel alignments
	  rank higher than indel alignments.

2009-05-05 02:46  twu

	* src/stage1hr.c: Computing floors between two segments in finding
	  middle indels

2009-05-04 14:41  twu

	* src/stage1hr.c: Added limit to number of middle indels found

2009-05-01 01:58  twu

	* src/stage1hr.c: Implemented incremental execution of fast
	  mismatch algorithm.

2009-05-01 01:19  twu

	* src/stage1hr.c: Fixed setting of indel separation in triage.
	  Prevented boostpos from being a compoundpos.	Turned off
	  tournament tree, since it was causing a crash.

2009-05-01 01:18  twu

	* src/spanningelt.c: Fixed bug occurring when all spanningelts have
	  no positions

2009-04-30 07:17  twu

	* src/stage1hr.c: Fixed bug with setting mismatch levels for
	  suboptimal results.  Solving all multiple_mm solutions in a
	  single run.

2009-04-30 06:56  twu

	* src/stage3hr.c: Fixed bugs in Stage3_remove_duplicates

2009-04-30 05:14  twu

	* src/stage3hr.h: Added function for counting number of optimal
	  hits.

2009-04-30 05:14  twu

	* src/stage3hr.c: Fixed problem with undesired removal of second
	  splice site within a given genomic region.  Added function for
	  counting number of optimal hits.

2009-04-30 05:12  twu

	* src/stage1hr.c: Removed code for REFINE_MISSES.  Added back
	  missing statement setting duplicates_possible_p.

2009-04-30 05:07  twu

	* src/gsnap.c: Removed minlevel and maxlevel and replaced with
	  suboptimal mismatches.  Made sort always happen.  Changed flag
	  name from invertp to circular-output.

2009-04-30 02:40  twu

	* src/: stage1hr.c, stage3hr.c, stage3hr.h: Using score in sorting
	  procedure.  Added provision for minlevel in Stage3_optimal_score.

2009-04-30 02:08  twu

	* src/: stage1hr.c, stage1hr.h: Refined miss_querypos5 and
	  miss_querypos3 boundaries.  Implemented triage for
	  minlevel_mismatches and maxlevel_mismatches instead of minlevel
	  and maxlevel, and accounted for fast mismatch algorithm.

2009-04-27 03:12  twu

	* src/gmapindex.c: Allowing contigs with a single nucleotide

2009-04-26 10:56  twu

	* src/: spanningelt.c, spanningelt.h: Removed boosterset idea and
	  returning only the minscore within the spanningset.

2009-04-26 10:55  twu

	* src/stage1hr.c: Removed all recursion from
	  identify_multimiss_iter.  Added feature to modify spanningset
	  list and update a counter when a spanningelt is empty.  Removed
	  boosterset idea and restored a single boostpos.  Correctly
	  implemented fast multimiss algorithm.

2009-04-26 01:27  twu

	* src/: spanningelt.c, spanningelt.h, stage1hr.c: Created separate
	  scores for candidate generation and for pruning.  Implemented
	  idea of a boosterset, instead of a single boostpos, but seems to
	  be slower.

2009-04-25 16:21  twu

	* src/: Makefile.dna.am, Makefile.gsnaptoo.am, indexdb_hr.c,
	  indexdb_hr.h, spanningelt.c, spanningelt.h, stage1hr.c: Created
	  formal Spanningelt_T object and rewrote algorithms to use it.

2009-04-24 04:33  twu

	* src/stage1hr.c: Preliminary implementation of a multimiss
	  algorithm generalized from the onemiss algorithm.

2009-04-23 08:23  twu

	* src/stage3hr.c: Fixed bug that resulted in duplicate outputs

2009-04-23 08:23  twu

	* src/stage1hr.c: Reverting to previous version

2009-04-23 08:23  twu

	* src/stage1hr.c: Implemented vertical solution for
	  find_segments_multiple_mm, which handles each querypos one at a
	  time, but result is much slower.

2009-04-23 02:54  twu

	* src/stage1hr.c: Removed code from before DELAY_READING.
	  Implemented tournament trees, which require slightly fewer
	  instructions than heaps.

2009-04-22 05:33  twu

	* src/: Makefile.gmaponly.am, Makefile.pmaptoo.am: Included
	  changepoint files.

2009-04-22 05:32  twu

	* src/Makefile.dna.am: Included changepoint files.  Included
	  indexdb_dump program.

2009-04-22 05:31  twu

	* src/bigendian.c: Added code to output files in bigendian format

2009-04-22 05:31  twu

	* src/: stage3.c, stage3.h: Parameterized TRIM_END_PVALUE.  Fixed
	  map feature of GMAP for new IIT format.

2009-04-22 05:30  twu

	* src/stage3hr.c: Loosened criteria for duplicate hits that was
	  eliminating overlapping matches with the same number of
	  mismatches.

2009-04-22 05:25  twu

	* src/: indexdb_hr.c, indexdb_hr.h, stage1hr.c: Using
	  binary_threshold instead of parent_ndiagonals

2009-04-22 05:25  twu

	* src/indexdb.c: Fixed bug for bigendian machines

2009-04-22 05:24  twu

	* src/iitdef.h: Changed type of divsort to be int, apparently for
	  compiler warnings?

2009-04-22 05:24  twu

	* src/: iit-read.h, iit-read.c: Implemented algorithm for map
	  feature of GMAP to use new IIT format

2009-04-22 05:23  twu

	* src/gmap.c: Using divint crosstable for map feature.

2009-04-21 07:28  twu

	* src/stage1hr.c: Implemented a delay in converting positions to
	  diagonals until needed.

2009-04-08 03:29  twu

	* src/stage3.c: Using number of matches to trim ends, not total
	  length

2009-04-04 00:21  twu

	* src/: indexdb_hr.c, stage1hr.c: Made exact and sub-1 code work
	  correctly on bigendian machines without having to copy memory.

2009-04-03 03:23  twu

	* src/: gmap.c, stage3.c, stage3.h: Modified -H flag to let user
	  control minendexon length

2009-04-03 03:04  twu

	* src/stage1hr.c: Skipping computation on poly-A or poly-T
	  sequences

2009-04-02 10:09  twu

	* src/stage3.c: Added check for null pairs before generating
	  matchscores

2009-04-02 10:09  twu

	* src/: pair.c, pair.h: Revised procedures for producing
	  matchscores

2009-04-02 10:08  twu

	* src/gsnap.c: Adding number of paths to output.  Removed check for
	  inplace being possible.

2009-04-02 10:08  twu

	* src/snpindex.c: Added comment

2009-04-02 10:07  twu

	* src/: indexdb.c, indexdb.h: Removed procedures that create
	  sentinels.

2009-04-02 10:04  twu

	* src/indexdb_hr.c: Not using sentinels.  For compoundpos, always
	  reading in place and converting to bigendian when needed.

2009-04-02 10:04  twu

	* src/: stage1hr.h, stage1hr.c: Not using sentinels.  For exact and
	  sub:1, always reading in place and converting to bigendian when
	  needed.

2009-04-02 07:42  twu

	* src/stage1.c: Added limits on number of gregions to speed up
	  program

2009-04-02 07:41  twu

	* src/: stage3.c, stage3.h: Using changepoint algorithm and
	  iterative trimming of ends to improve ends of alignment.

2009-04-02 07:33  twu

	* src/: indexdb.c, indexdb.h: Added hooks for sentinel in indexdb
	  files

2009-04-02 07:26  twu

	* src/: gregion.c, gregion.h: Rewrote support filtering to use
	  either a fixed difference (for longer sequences) or a percentage
	  difference (for shorter ones).  For extending sequences, using
	  querylength for adequate support or short support.

2009-04-02 07:19  twu

	* src/gmap.c: Improved documentation for --help

2009-04-02 07:19  twu

	* src/genome-write.c: Always print out number of bad characters

2009-04-02 07:15  twu

	* src/: changepoint.c, changepoint.h: Modified procedures to ignore
	  -1 values in input

2009-03-31 01:53  twu

	* src/stage1hr.c: Using heaps for nomiss and onemiss, but not for
	  exact.  Replacing NULL lists with sentinels when necessary.

2009-03-31 01:42  twu

	* src/stage1.c: Implemented limit on number of gregions before
	  finding unique ones, to prune nonspecific, slow sequences.

2009-03-26 09:21  twu

	* src/stage1hr.c: Using pointers and relying on sentinels to
	  advance through lists.

2009-03-26 02:09  twu

	* src/stage1hr.c: Removed old code

2009-03-26 02:06  twu

	* src/stage1hr.c: Changed sub:1 recursive procedures to iterative

2009-03-26 01:29  twu

	* src/stage1hr.c: Reverting to previous version

2009-03-26 01:28  twu

	* src/stage1hr.c: Attempt to use information from third and later
	  lists to advance first list

2009-03-26 01:05  twu

	* src/stage1hr.c: Using results of second list to speed up
	  intersection

2009-03-25 15:00  twu

	* src/stage1hr.c: Implemented a faster version of performing
	  intersection for exact matches.

2009-03-25 13:09  twu

	* src/stage1hr.c: Starting exact matches with intersection of first
	  two lists.

2009-03-25 06:42  twu

	* src/stage1hr.c: Made non-heap compoundpos_find procedure the
	  default

2009-03-25 03:34  twu

	* src/: indexdb_hr.c, indexdb_hr.h: Implemented a non-heap version
	  of searching through a union of positions.

2009-03-25 02:31  twu

	* src/indexdb_hr.c: Added hooks for handling indexdb with
	  sentinels.  Removed unused code.

2009-03-25 02:24  twu

	* src/stage1hr.c: Implemented iterative version of find_exact_aux.
	  Depending on sentinel to increase speed of loop.

2009-03-24 06:11  twu

	* src/: gmap.c, pair.c, pair.h, stage3.c, stage3.h: Fixed printing
	  in psl format when user provides a segment

2009-03-24 06:10  twu

	* src/: compress.c, compress.h, genome-write.c: Fixed reporting of
	  non-ACGTNX characters

2009-03-24 05:32  twu

	* src/: gmap.c, stage3.c, stage3.h: Removed -k flag and trimexonpct
	  parameter

2009-03-24 05:22  twu

	* src/iit_fetch.c: Added ability to compute ratios from pdl files

2009-03-24 05:21  twu

	* src/: iit-read.c, iit-read.h: Provided procedures for dumping
	  version 1 IITs

2009-03-24 05:21  twu

	* src/get-genome.c: Fixed dump output of contigs

2009-03-24 05:20  twu

	* src/compress.c: Reduced number of error messages for non-ACGTNX
	  characters

2009-03-24 05:19  twu

	* src/stage3.c: No longer using non-canonical introns for trimming
	  end exons, only binomial test.  Fixed bad behavior for theta
	  values close to 1.0.	Not reporting alignments with fewer than 20
	  matches.

2009-03-19 03:53  twu

	* src/iit_fetch.c: Added hook for splices iits

2009-03-19 03:30  twu

	* src/: plotgenes.c, plotgenes.h: Added function for handling
	  splices.  Made sure nbins > 0.

2009-03-18 10:42  twu

	* src/: plotgenes.c, plotgenes.h: Added function
	  Plotgenes_fetch_points.  Renamed some functions.

2009-03-18 06:57  twu

	* util/gmap_setup.pl.in: Gives files on command line to fa_coords
	  and gmap_process, which can then add linefeed if necessary to
	  lines.

2009-03-18 06:56  twu

	* util/gmap_process.pl.in: Allowed program to read from either
	  stdin or files on command line.  In the latter case, it adds
	  linefeed if necessary to lines.

2009-03-18 06:56  twu

	* util/fa_coords.pl.in: Re-indented program.  Allowed program to
	  read from either stdin or files on command line.

2009-03-18 04:53  twu

	* src/iit_fetch.c: Implemented handling of PDL files.  Added -s
	  flag to specify sample number.

2009-03-18 04:53  twu

	* src/stage3.c: Trimming using a binomial test on end exons

2009-03-18 04:50  twu

	* src/: snpindex.c, gdiag.c, genome.c, genome.h, get-genome.c,
	  gsnap-to-iit.c, gsnap.c, indexdb.c, indexdb.h, oligo-count.c:
	  Modified programs to take a snp_root argument to -V

2009-03-18 04:49  twu

	* src/gmap.c: Added "Processed" message to stderr at end of batch
	  run

2009-03-18 04:48  twu

	* src/: Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am, Makefile.pmaptoo.am: Updated Makefiles

2009-03-18 04:47  twu

	* src/: pair.c, pair.h: Added function Pair_fracidentity_simple

2009-03-18 04:47  twu

	* src/: pbinom.c, pbinom.h: Initial import into CVS

2009-03-17 09:15  twu

	* src/gsnap.c: Considering too many paths as a failure type for the
	  --nofails and --failsonly flags

2009-03-10 09:19  twu

	* src/stage1.c: Added variable needed in debugging

2009-03-10 09:19  twu

	* src/: plotgenes.c, plotgenes.h: Renamed functions relating to
	  fetching

2009-03-10 09:19  twu

	* src/iit_fetch.c: Removed code relating to printing

2009-03-10 09:19  twu

	* src/iit-read.c: Fixed issues for bigendian machines and for
	  fileio access

2009-03-10 09:18  twu

	* src/: datadir.c, datadir.h, gmap.c: Added extra functionality to
	  show available databases and map files

2009-03-10 08:10  twu

	* src/iit_fetch.c: Initial import into CVS.  Copied from iit_plot.c

2009-03-10 02:21  twu

	* src/: iit-read.c, iit-write.c, indexdb.c, indexdb_hr.c,
	  intpool.c, oligo.c, oligoindex.c, oligoindex.h, pair.c, reader.c,
	  sequence.c, smooth.c, stage1.c, stage2.c, stage3.c,
	  translation.c, blackboard.c, changepoint.c, compress.c, diag.c,
	  dynprog.c, genome-write.c, genome.c, get-genome.c, gmap.c,
	  gmapindex.c, gregion.c: Removed unused variables based on SGI
	  compiler warnings

2009-03-09 10:27  twu

	* src/iit-read.c: Fixed reading of labels and annotations using
	  fileio on bigendian machines.

2009-03-09 10:26  twu

	* src/: bigendian.c, bigendian.h: Added command for reading uint
	  using fileio

2009-03-09 08:54  twu

	* src/stage3.c: Fixed bug where gap was left at 3' end before
	  extending the end.

2009-03-09 08:53  twu

	* src/stage1hr.c: Fixed counting of mismatches on revcomp sequences

2009-03-09 08:53  twu

	* src/indexdb_hr.c: Made heapsize an int, rather than unsigned int,
	  in all procedures

2009-03-09 08:52  twu

	* src/indexdb.c: Moved variable declarations above debugging
	  statement to satisfy SGI compiler.

2009-03-09 08:52  twu

	* src/gsnap.c: Changed variable names involving -q flag to "part_"

2009-03-09 08:51  twu

	* src/: iit_get.c, get-genome.c: Printing divstring only if ndivs >
	  1

2009-03-09 08:50  twu

	* src/iit-read.h: Added ability to retrieve divstring from
	  universal coordinates.

2009-03-09 08:50  twu

	* src/iit-read.c: Added ability to retrieve divstring from
	  universal coordinates.  Fixed bug occurring during reading
	  annotatinos using fileio.

2009-03-09 03:00  twu

	* src/iit-write.c: Fixed bug relating to use of null annotlist to
	  indicate altstrain IIT.

2009-03-06 04:15  twu

	* src/: stage3.c, pair.c, pair.h: Fixed bug where -P and -Q flags
	  were printing C-to-N on antisense cDNAs.

2009-02-20 06:42  twu

	* util/gmap_setup.pl.in: Added FILE_ENDINGS variable

2009-02-20 06:41  twu

	* src/get-genome.c: Removed debugging flag

2009-02-20 06:40  twu

	* src/sequence.c: Improved handling of blank lines

2009-02-20 06:24  twu

	* src/: indexdb.c, snpindex.c: Changed offsets and positions to
	  occur at modulo 0 intervals based on chrpos, not universal
	  position.

2009-02-20 06:20  twu

	* src/iit_get.c: Added feature to print results from tally types of
	  IITs

2009-02-20 06:20  twu

	* src/iit-read.c: Fixed bug in re-fetching matches based on index

2009-02-20 06:19  twu

	* src/gsnap.c: Cleared flags for batch and novelsplicing

2009-02-20 06:19  twu

	* src/types.h: Removed an extraneous open brace

2009-02-20 06:19  twu

	* src/: stage3hr.c, stage3hr.h: Calculating splice site model score
	  at print time for all splice sites.

2009-02-20 06:18  twu

	* src/stage1hr.c: Providing sense information for donor and
	  acceptor substrings.	Testing if duplicate matches are possible
	  due to minlevel and eliminating them.

2009-02-05 07:30  twu

	* src/: stage3hr.c, stage3hr.h: Distinguishing between splice
	  objects that require copying of substrings and those that do not.

2009-02-05 07:30  twu

	* src/stage1hr.c: Incorporated splice site probabilities into
	  finding splice sites by distance.

2009-02-05 05:30  twu

	* src/stage1hr.c: Initial implementation of finding splice pairs by
	  distance

2009-02-05 01:31  twu

	* src/gsnap.c: Retrieving and printing known splicesite information
	  at print time.

2009-02-05 01:30  twu

	* src/: iit-read.c, iit-read.h: Added function
	  IIT_get_typed_with_divno

2009-02-05 01:30  twu

	* src/: stage3hr.c, stage3hr.h: Providing chroffset information to
	  Substring_T object.  Retrieving and printing known splicesite
	  information at print time.

2009-02-05 01:29  twu

	* src/stage1hr.c: Providing chroffset information to Substring_T
	  object

2009-02-04 09:44  twu

	* src/: stage1hr.h, stage1hr.c: Implemented faster method for
	  applying known splice sites

2009-02-04 09:36  twu

	* src/gsnap.c: Implemented faster method for applying known splice
	  sites

2009-02-04 07:06  twu

	* src/: stage1hr.c, stage1hr.h: Fixed bug when allvalidp5 or
	  allvalidp3 is false in paired end reads.  Implemented
	  Stage1_retrieve_splicesites.

2009-02-04 07:05  twu

	* src/: resulthr.c, resulthr.h: Renamed paired_translocation as
	  paired_as_singles

2009-02-04 07:05  twu

	* src/iit-read.c: Fixed bug in evaluating nexactmatches

2009-02-04 07:04  twu

	* src/get-genome.c: Made retrieval of map information work with
	  universal coordinates.

2009-02-04 05:01  twu

	* src/stage3hr.c: Fixed bug where second read of paired_as_singles
	  was not being printed

2009-02-04 05:00  twu

	* src/gsnap.c: Renamed paired_translocation to paired_as_singles

2009-02-03 09:02  twu

	* src/genome_hr.c: Now requiring query to match either reference or
	  alternate allele at SNPs.  Otherwise, it counts as a mismatch.

2009-02-02 15:19  twu

	* src/get-genome.c: Added feature to print snp information

2009-02-02 15:18  twu

	* src/: iit_plot.c, gsnap-to-iit.c, gdiag.c: Using new interface to
	  Genome_new

2009-02-02 15:17  twu

	* src/stage3hr.c: Eliminating novel splice site when it duplicates
	  a known splice site

2009-02-02 15:16  twu

	* src/stage1hr.c: Fixed bug where plus multiple mismatches are
	  dropped when minus batches are all empty.  Added flexibility to
	  floor_xfirst and floor_xlast to allow for indels adjacent to end
	  12-mers.  Changed condition endpoint for indels at ends.  Using
	  genome_hr procedure to count mismatches for indels.  Finding all
	  shortdistance splices with known splice sites first, before
	  finding novel splice sites.

2009-02-02 15:12  twu

	* src/snpindex.c: Writing revised version of genome.  Skipping
	  cases where snp type is inconsistent with reference genome.
	  Taking snps_iit as a command-line argument.

2009-02-02 15:10  twu

	* src/: sequence.c, sequence.h: Added Sequence_print_two function
	  for snps

2009-02-02 15:10  twu

	* src/gsnap.c: Using genomealt instead of snps_iit

2009-02-02 15:09  twu

	* src/gmap.c: Switched -v and -V flags.  Using new interface to
	  Genome_new.

2009-02-02 15:09  twu

	* src/genome_hr.c: Corrected calculation of mismatches_right.
	  Corrected offset and now subtracting number of leading zeroes.
	  Using clz_table instead of log_table.  Improved debugging
	  statements.

2009-02-02 05:36  twu

	* src/: genome_hr.c, genome_hr.h, stage1hr.c, stage1hr.h: Using
	  genomealt instead of snps_iit

2009-02-02 05:35  twu

	* src/: genome.c, genome.h: Added ability to read Genome_T object
	  as alternate or snp only versions.

2009-02-01 11:26  twu

	* src/: oligo-count.c, gdiag.c: Using new interface to
	  Indexdb_new_genome

2009-02-01 11:25  twu

	* src/: indexdb.c, indexdb.h: Storing positions only at 0 mod 3.

2009-02-01 11:24  twu

	* src/gsnap.c: Made batch loading the default for multiple input
	  sequences.  Testing for both new names and old names of reference
	  offsets and positions files.	Made flag for splicing refer to
	  novel splicing.

2009-02-01 11:23  twu

	* src/: gmapindex.c, pmapindex.c: Removed altstrain code

2009-02-01 11:22  twu

	* src/gmap.c: Made batch loading the default for multiple input
	  sequences.  Testing for both new names and old names of reference
	  offsets and positions files.

2009-02-01 11:21  twu

	* src/get-genome.c: Added debugging statement

2009-02-01 11:21  twu

	* src/genome_hr.c: Fixed retrieval of intervals from snps_iit file,
	  which are 1-based.

2009-02-01 11:18  twu

	* src/: stage1hr.c, stage1hr.h: Implemented snp differences for
	  splicing and exact matches.  Allowing identification of novel
	  splicing in addition to known splice sites.

2009-02-01 11:17  twu

	* src/stage3hr.c: Implemented reporting of snp differences for
	  indels.

2009-02-01 10:37  twu

	* src/snpindex.c: Fixed bug in using chromosomal position instead
	  of universal position.  Using parameterized suffix for reference
	  offsets and positions files.

2009-01-29 22:08  twu

	* src/snpindex.c: Initial import into CVS

2009-01-28 13:24  twu

	* src/genome_hr.c: In Genome_mismatches_left and
	  Genome_mismatches_right, adding a 'sentinel' mismatch position to
	  list if haven't reached max_mismatches.

2009-01-28 13:23  twu

	* src/stage1hr.c: Implemented tolerance and reporting of snp
	  differences for novel splice sites.

2009-01-28 02:33  twu

	* src/: stage3hr.c, stage3hr.h: Added ability to print number of
	  SNP differences separately.  Thie feature not yet implemented for
	  indels though.

2009-01-28 02:32  twu

	* src/: stage1hr.c, stage1hr.h: Added ability to tolerate known
	  SNPs and count differences at those sites separately.  Thie
	  feature not yet implemented for novel splices though.

2009-01-28 02:32  twu

	* src/: segmentpool.c, segmentpool.h: Changed name of chrlow to
	  chroffset

2009-01-28 02:31  twu

	* src/iit-read.c: Fixed computation of divint_crosstable

2009-01-28 02:31  twu

	* src/: genome_hr.c, genome_hr.h, gsnap.c: Added ability to
	  tolerate known SNPs and count differences at those sites
	  separately.

2009-01-27 08:42  twu

	* src/gsnap-to-iit.c: Increased buffer sizes

2009-01-27 08:42  twu

	* src/get-genome.c: Made get-genome work on map files

2009-01-27 08:42  twu

	* src/plotgenes.c: Edited comments

2009-01-27 08:41  twu

	* src/gsnap.c: Provided user with the ability to set parameters for
	  size of middle and end insertions and deletions.

2009-01-22 05:54  twu

	* src/stage1hr.c: Added steps to remove duplicate paired-end
	  results

2009-01-22 05:18  twu

	* src/stage1hr.c: Fixed memory leak

2009-01-22 05:18  twu

	* src/gsnap.c: Increased default maxpaths from 20 to 100.  Added -e
	  flag to --help output.  Providing max_mismatches parameter to
	  paired-end procedure.

2009-01-22 05:16  twu

	* src/stage3hr.h: Added function Stage3_remove_old.

2009-01-22 05:16  twu

	* src/stage3hr.c: Revised definition of paired-end length to go
	  from beginning-of-read to beginning-of-read.	Added function
	  Stage3_remove_old.

2009-01-22 02:14  twu

	* src/: stage1hr.c, stage1hr.h: Passing max_mismatches parameter
	  for paired reads

2009-01-21 09:17  twu

	* src/indexdb_hr.c: Fixed bug where heapify was performed after
	  binary_search used up all available diagonals in a batch.

2009-01-21 05:42  twu

	* util/gmap_setup.pl.in: Fixed bug in escaping a variable

2009-01-21 05:35  twu

	* config/pagesize.m4: Made comment line clearer

2009-01-21 05:34  twu

	* config/builtin.m4: Initial import into CVS.

2009-01-21 05:31  twu

	* util/Makefile.am: Added gmap_reassemble

2009-01-21 05:30  twu

	* util/fa_coords.pl.in: Made -S flag the default.  Added -C flag to
	  look explicitly for chromosomal information.

2009-01-21 05:29  twu

	* util/md_coords.pl.in: Added check for unmapped contigs

2009-01-21 05:28  twu

	* util/gmap_setup.pl.in: Maded -S flag the default behavior.  Added
	  -C and -O flags.  Added clean procedure when making
	  coords.genome.

2009-01-21 05:26  twu

	* src/: stage3hr.c, stage3hr.h: Including label as part of
	  Substring_T

2009-01-21 05:25  twu

	* src/stage1hr.h: Added procedures for finding splices against
	  known splicesites iit.

2009-01-21 05:25  twu

	* src/stage1hr.c: Added procedures for finding splices against
	  known splicesites iit.  Corrected computation of distances on
	  inversions.

2009-01-21 05:23  twu

	* src/indexdb.c: Cleaned code to ensure gsnap finds the right
	  offsets file

2009-01-21 05:22  twu

	* src/iit-write.c: Added check for a null typestring

2009-01-21 05:22  twu

	* src/iit_dump.c: Fixed debugging output

2009-01-21 05:22  twu

	* src/iit-read.h: Added procedures to search based on divint and to
	  get a crosstable of divints.

2009-01-21 05:21  twu

	* src/iit-read.c: Fixed IIT_debug.  Added procedures to search
	  based on divint and to get a crosstable of divints.

2009-01-21 05:20  twu

	* src/gsnap.c: Added flags for maxmismatches, splicing penalties,
	  and splicing iit.  Added flags for failsonly and nofails in
	  output.

2009-01-21 05:19  twu

	* src/gregion.c: Added abort if genomicend < genomicstart

2009-01-21 05:18  twu

	* src/gmapindex.c: Eliminated reading of strain information and
	  assignment to contigtypelist.  Increased size of chrpos string
	  from 100 to 8192.

2009-01-21 05:17  twu

	* src/gmap.c: Reformatted output for --help

2009-01-15 05:01  twu

	* src/stage1hr.c: Created user-specified parameters for splicing
	  probabilities and length.

2009-01-15 04:53  twu

	* src/stage1hr.c: Fixed bug in printing coordinates of splicing
	  results on minus strand

2009-01-14 06:09  twu

	* src/gsnap.c: Added flags for excluding failed alignments, or
	  limiting to those

2009-01-13 02:17  twu

	* src/stage1hr.c: Added additional check to prevent straddling
	  across chromosomes

2009-01-13 01:33  twu

	* src/: stage1hr.c, indexdb_hr.c, indexdb_hr.h: Implemented more
	  efficient way of ignoring extensions past beginning of genome.

2009-01-07 14:42  twu

	* src/stage1hr.c: Hacks put in to exclude diagonals that are less
	  than querylength

2009-01-07 14:27  twu

	* src/stage1hr.c: Fixed issues with wrong indel_pos chosen in
	  middle insertions, and not checking up to specified number of
	  indels.

2008-12-24 03:35  twu

	* src/indexdbdef.h: Reverted to version 1.2

2008-12-24 03:34  twu

	* src/indexdb.c: Reverted to version 1.121

2008-12-24 03:33  twu

	* src/: indexdb.c, indexdbdef.h: Attempt to use a compressed
	  indexdb file

2008-12-22 03:35  twu

	* src/stage1hr.c: Reading floor 2 during find_segments_multiple_mm.
	  Returning min_mismatches_seen from find_onemiss_matches.

2008-12-21 09:07  twu

	* src/indexdb_hr.c: Put check for size of compoundpos outside of
	  loop.

2008-12-21 09:06  twu

	* src/stage1hr.c: Added bounds on location of mismatch in onemiss
	  search

2008-12-21 05:51  twu

	* src/stage1hr.c: Reverted back to version 1.106 that has hanging
	  compoundpos positions for exact and onemiss matches.

2008-12-21 05:49  twu

	* src/stage1hr.c: Version of stage 1 with hooks for disallowing
	  compoundpos positions that hang over ends.  However, this appears
	  to add 40% to number of instructions.

2008-12-20 15:47  twu

	* src/stage1hr.c: Setting pointers->compoundpos to NULL after it
	  becomes empty, to prevent further computation on it.

2008-12-20 13:10  twu

	* src/: indexdb_hr.c, indexdb_hr.h: Added function
	  Compoundpos_intersect

2008-12-20 13:10  twu

	* src/stage1hr.c: Eliminated compoundpos positions in creating
	  segments from multiple mismatches.  Delayed sorting of segments
	  until needed for middle insertions and deletions.  Setting floor
	  to zero in cases where poly-AT is present.  For end indels,
	  computing oligomer_start and oligomer_end based on results of
	  actual mismatches found.

2008-12-20 00:20  twu

	* src/stage1hr.c: Fixed bug in debugging statement

2008-12-20 00:19  twu

	* src/gmapindex.c: Added more compiler checks to hide alternate
	  strain code

2008-12-20 00:19  twu

	* src/Makefile.util.am: Added program all-orfs

2008-12-20 00:18  twu

	* src/: Makefile.dna.am, Makefile.gsnaptoo.am: Removed chrsubset.c
	  from gsnap sources

2008-12-18 15:30  twu

	* src/: stage3hr.c, stage3hr.h: Using left instead of genomicpos5
	  for creating Stage3_T objects.

2008-12-18 15:29  twu

	* src/stage1hr.c: Using left instead of genomicpos5 for creating
	  Stage3_T objects.  Consolidated code for plus and minus segments.
	  Changed parameter list for find_segments_multiple_mm to prepare
	  for finding hits within that procedure.

2008-12-18 10:46  twu

	* src/stage1hr.c: Clarified calculations of floors

2008-12-17 06:11  twu

	* src/stage1hr.c: Using init and search routines for Compoundpos_T
	  objects

2008-12-17 06:11  twu

	* src/separator.h: Changed coordinate separator from "--" to ".."

2008-12-17 06:10  twu

	* src/: intlist.c, intlist.h: Added function
	  Intlist_sort_ascending()

2008-12-17 06:10  twu

	* src/: indexdb_hr.c, indexdb_hr.h: Implemented init and search
	  routines for Compoundpos_T objects

2008-12-17 06:09  twu

	* src/: iit-write.c, iit_store.c: Added monitoring output

2008-12-16 20:06  twu

	* src/stage1hr.c: Clarified processing of pointers in search for
	  onemiss matches.

2008-12-16 14:15  twu

	* src/stage1hr.c: Allowing spanning 12-mers for exact and onemiss
	  searches to go in either forward or reverse direction, and
	  picking the optimal direction.

2008-12-16 12:33  twu

	* src/stage1hr.c: Allowing compoundpos positions to be used for
	  boosting, by merging them during search for exact matches.

2008-12-16 12:32  twu

	* src/stage1.c: Fixed a bug where the querypos of sentinel was set
	  incorrectly.	Now using querylength, not -1.	Added a check to
	  prevent gregions with negative values for genomicstart.

2008-12-16 10:59  twu

	* src/: indexdb_hr.c, indexdb_hr.h: Removed partner_diagonals from
	  Compoundpos_T object and removed reduce function.

2008-12-16 10:58  twu

	* src/stage1hr.c: Fixed potential problem with sentinel.  The
	  querypos part of sentinel now set to querylength, not -1, to
	  guarantee it stops the loop.	Introduced Pointers_T object to
	  simplify exact and onemiss code.

2008-12-15 13:06  twu

	* src/stage1hr.c: Introduction of Compoundpos_T object for speeding
	  up computation in exact and onemiss algorithms

2008-12-15 13:05  twu

	* src/: intlist.c, intlist.h: Added Intlist_insert_second()
	  function

2008-12-15 13:05  twu

	* src/: indexdb_hr.c, indexdb_hr.h: Introduction of Compoundpos_T
	  object and operations

2008-12-14 13:34  twu

	* src/intlist.c: Made cell_ascending() and cell_descending()
	  static.

2008-12-14 13:33  twu

	* src/: genome_hr.c, genome_hr.h: Created
	  Genome_count_mismatches_limit.  Also added code for a oneloop
	  version of Genome_count_mismatches.

2008-12-14 13:32  twu

	* src/gsnap.c: Removed chrsubset feature

2008-12-14 13:32  twu

	* src/: stage3hr.c, stage3hr.h: Clarified that Substring_new_donor
	  and Substring_new_acceptor should receive forward query sequence.

2008-12-14 13:31  twu

	* src/stage1hr.c: Removed querylength from call to
	  select_positions_for_exact().

2008-12-14 09:42  twu

	* src/stage1hr.h: Removed Chrsubset_T object.

2008-12-14 09:42  twu

	* src/stage1hr.c: Using new call to Genome_count_mismatches_limit.
	  Replaced uses of queryseq with queryuc_ptr and queryrc.
	  Introduced query_lastpos to replace multiple calculations of
	  (querylength - INDEX1PART).  Removed Chrsubset_T object.

2008-12-14 01:14  twu

	* src/stage1hr.c: Fixed onemiss algorithm so it handles short reads
	  less than 2*INDEX1PART in length.  Changed occurrences of
	  oligobase to INDEX1PART.  Removed oligobase and querylength from
	  Stage1_T object.

2008-12-13 16:52  twu

	* src/: genome_hr.c, genome_hr.h: Made Genome_count_mismatches more
	  efficient, by using pointers and stepping through query and
	  genome blocks sequentially.

2008-12-13 03:00  twu

	* src/stage1hr.c: Implemented new method for identifying single
	  mismatches, similar to that for finding exact matches.

2008-12-12 10:06  twu

	* src/result.h: Added a new failure type for short sequences

2008-12-12 10:06  twu

	* src/pmapindex.c: Changed default index1interval from 3 to 6

2008-12-12 10:06  twu

	* src/oligo.c: Added a comment.

2008-12-12 10:05  twu

	* src/oligo-count.c: Using revised interface to indexdb.c.

2008-12-12 10:05  twu

	* src/: indexdb_hr.c, indexdb_hr.h: Removed addition of a diagterm
	  for lookups involving a left or right shift.

2008-12-12 10:04  twu

	* src/: indexdb.c, indexdb.h: Changed some function names.  Added
	  function to determine if inplace reading is possible.  Added
	  parameter to require sampling of 3 in indexdb.

2008-12-12 10:03  twu

	* src/gmap.c: Using revised interface to indexdb.c.  Added check
	  and message for sequences shorter than INDEX1PART.

2008-12-12 10:02  twu

	* src/gdiag.c: Using revised interface to indexdb.c

2008-12-12 10:02  twu

	* src/block.c: Using revised function names in indexdb.c

2008-12-12 10:01  twu

	* src/: segmentpool.c, segmentpool.h: Removed break5 and break3
	  from Segmentpool_T object.

2008-12-12 10:00  twu

	* src/stage1hr.c: Removed break5 and break3 from Segmentpool_T
	  object

2008-12-12 10:00  twu

	* src/stage1.c: Providing correct adjustment to diagonals for the
	  minus strand, by adding the length of the oligomer.

2008-12-12 07:47  twu

	* src/: stage3hr.c, stage3hr.h: Added function to compare Stage3_T
	  objects by genomic location

2008-12-12 07:46  twu

	* src/gsnap.c: Added flag to sort results by genomic location

2008-12-12 07:46  twu

	* src/stage1hr.c: No longer saving segments during check for single
	  mismatches.  Checking and saving substitution hits within each
	  heap merge.

2008-12-12 03:11  twu

	* src/gsnap.c: Added user flag for setting indel penalty

2008-12-12 03:11  twu

	* src/: stage1hr.c, stage1hr.h: Made indel_penalty a parameter
	  adjustable by the user.

2008-12-11 07:59  twu

	* src/stage1hr.c: Moved around code for special cases that prevent
	  searching for end indels at beginning or end of the sequence.

2008-12-11 07:58  twu

	* src/gsnap.c: Added information about whether inplace reading of
	  indexdb is possible.	Added information to version command.

2008-12-11 05:12  twu

	* src/: segmentpool.c, segmentpool.h: Added floor, floor_xfirst,
	  and floor_xlast fields to the Segment_T object.

2008-12-11 05:12  twu

	* src/stage1hr.c: Removed separate lists of segments by floor.
	  Keeping only a single list of plus segments and of minus
	  segments, with floor information stored in the Segment_T object.

2008-12-11 04:31  twu

	* src/stage1hr.h: Providing information about whether inplace
	  reading of diagonals is possible.

2008-12-11 04:30  twu

	* src/stage1hr.c: Delayed addition of diagterm until after search
	  for exact matches.  Allowing reads of diagonals from indexdb to
	  be inplace when possible

2008-12-10 12:51  twu

	* src/types.h: Added check for size of unsigned long long as an
	  8-byte word

2008-12-10 12:51  twu

	* src/stage1hr.c: Using 64-bit words, if available, to speed up
	  comparison of batches in heap merge.

2008-12-10 08:58  twu

	* src/stage1hr.c: Replaced calls to List_head, List_next,
	  Intlist_head, and Intlist_next with primitives.

2008-12-10 07:55  twu

	* src/Makefile.pmaptoo.am: Revised source files

2008-12-10 07:54  twu

	* src/Makefile.gsnaptoo.am: Added gsnap-to-iit program.  Added
	  segmentpool.

2008-12-10 07:54  twu

	* src/Makefile.gmaponly.am: Added chrom.c to iit utilities

2008-12-10 07:53  twu

	* src/Makefile.dna.am: Removed test programs for Compress_T
	  procedures

2008-12-10 07:52  twu

	* src/Makefile.dna.am: Added test programs for Compress_T
	  procedures.  Added segmentpool.

2008-12-10 07:51  twu

	* src/: segmentpool.c, segmentpool.h: Initial import into CVS

2008-12-10 07:49  twu

	* src/: gsnap.c, stage1hr.c, stage1hr.h: Added segmentpool

2008-12-09 10:09  twu

	* src/stage1hr.c: Enforcing diagonals to be within chromosomal
	  bounds.  Removed unused code.

2008-12-09 10:08  twu

	* src/genome.c: Fixed check for chromosome bounds

2008-12-09 10:07  twu

	* src/: genome_hr.c, genome_hr.h: Removed checks for crossing of
	  chromosome boundaries.  Relying upon calling procedures to
	  enforce this.

2008-12-08 07:58  twu

	* src/gsnap.c: Added flags for minlevel and maxlevel.  Cleaned up
	  unused flags.

2008-12-08 07:57  twu

	* src/: genome_hr.c, genome_hr.h: Made functions return maximum
	  number of mismatches if they cross a chromosome bound.

2008-12-05 02:02  twu

	* src/stage1hr.c: On end indels, checking to see if indel_pos is
	  non-positive.  Passing chromosome_iit to Genome_mismatches_left
	  and Genome_mismatches_right.

2008-12-05 02:00  twu

	* src/gsnap.c: Added statement at end of batch processing to
	  indicate number of queries processed.

2008-12-02 08:23  twu

	* src/subseq.c: Added U and l flags

2008-12-02 08:23  twu

	* src/stage1hr.c: For middle indels, putting indel at leftmost
	  genomic position.  Fixed filtering criteria for end indels.
	  Counting mismatches and left and right to identify candidates for
	  end indels.

2008-12-02 08:21  twu

	* src/stage1.c: Added debugging statements

2008-12-02 08:20  twu

	* src/gmap.c: Fixed genomiclength for user-provided genomic
	  sequence.  Stopped trimming of sequence.

2008-12-02 08:19  twu

	* src/: gdiag.c, gsnap-to-iit.c: Using new interface to
	  Genome_fill_buffer

2008-12-02 08:19  twu

	* src/diag.c: Loosened criteria for MAX_DIAGONALS and MIN_SCORE.

2008-11-25 09:33  twu

	* src/genome_hr.c: Made Genome_mismatches_left and
	  Genome_mismatches_right fill mismatch_positions entries
	  0..max_mismatches.

2008-11-25 09:32  twu

	* src/stage1hr.c: Implemented new algorithms for middle insertions
	  and deletions, using Genome_mismatches_left and
	  Genome_mismatches_right.

2008-11-25 01:46  twu

	* src/stage1hr.c: Using new interface to Genome_count_mismatches

2008-11-25 01:45  twu

	* src/: genome_hr.c, genome_hr.h: Added functions
	  Genome_mismatches_left and Genome_mismatches_right.  Added
	  builtin bit-vector functions.

2008-11-24 13:44  twu

	* src/: genome_hr.c, genome_hr.h: Allowed specification of pos5 and
	  pos3 in Genome_count_mismatches

2008-11-24 07:30  twu

	* src/genome_hr.h: Using new Compress_T object.

2008-11-24 07:29  twu

	* src/genome_hr.c: Using new Compress_T object.  Removed unused
	  code.

2008-11-24 07:29  twu

	* src/stage1hr.c: Using new Compress_T object

2008-11-24 07:28  twu

	* src/stage3hr.c: Fixed memory leak

2008-11-24 07:28  twu

	* src/: compress.c, compress.h: Introduced Compress_T object

2008-11-23 11:04  twu

	* src/: genome_hr.c, genome_hr.h: Initial entry into CVS

2008-11-23 11:04  twu

	* src/gsnap.c: Added flag for handling circular-end reads

2008-11-23 11:03  twu

	* src/: stage3hr.c, stage3hr.h: Making a single invertp work on
	  paired-end and circular-end reads

2008-11-23 11:02  twu

	* src/stage1hr.c: Using direct comparison against compressed genome
	  to count mismatches

2008-11-23 11:01  twu

	* src/: genome.c, genome.h: Added function Genome_blocks.  Made
	  Genome_fill_buffer return nunknowns.

2008-11-23 11:00  twu

	* src/: compress.c, compress.h: Added functions Compress_new and
	  Compress_shift

2008-11-20 02:16  twu

	* src/: sequence.c, sequence.h: For circular-end reads, keeping
	  reverse complement of queryseq2, but swapping queryseq1 and
	  queryseq2.

2008-11-20 02:14  twu

	* src/stage1hr.h: Placed local exon-exon mappings after multiple
	  substitutions and indels in the hierarchy of levels.

2008-11-20 02:13  twu

	* src/stage2.c: Commented out unused procedure

2008-11-20 02:13  twu

	* src/stage3.c: Added debugging statement

2008-11-20 02:12  twu

	* src/: stage3hr.c, stage3hr.h: Enabled printing of circular-end
	  reads

2008-11-13 09:27  twu

	* src/stage1hr.c: Allowing mismatches with splicing

2008-11-11 08:39  twu

	* src/: stage1hr.h, gsnap.c: Removed unused parameters

2008-11-11 08:39  twu

	* src/stage1hr.c: Using new single-end read algorithms for
	  paired-end reads.  Fixed problems with query sequences that
	  contain non-ACGT characters.

2008-11-11 08:38  twu

	* src/stage3hr.c: Fixed problems with printing inverted sequence
	  for paired-end reads

2008-11-11 04:37  twu

	* util/gmap_reassemble.pl.in: Initial entry into CVS

2008-11-11 04:30  twu

	* src/stage3hr.c: Fixed bug in Stage3_remove_duplicates

2008-11-11 04:29  twu

	* src/stage1hr.c: Revised splicing parameters.	Fixed calculation
	  of maxfloor.

2008-11-10 05:17  twu

	* src/stage3hr.c: Favoring substitutions over equivalent indels in
	  removing repeats.

2008-11-10 05:16  twu

	* src/stage1hr.c: Treating max_middle_insertions and
	  max_middle_deletions separately in solving middle indels.
	  Removed scores from compute_end_indels.  Not resetting
	  min_mismatches after single_mm, because of effect of poly_at
	  oligos.

2008-11-10 03:46  twu

	* src/stage3hr.c: Added check and warning messages if observed
	  mismatches is different from the number expected

2008-11-10 03:45  twu

	* src/: stage1hr.h, gsnap.c: Allowing separate parameters for
	  middle and end insertions and deletions.

2008-11-10 03:45  twu

	* src/stage1hr.c: Introduced floor system for computing indels.
	  Defined calculation of middle and end indels more clearly, with
	  separate parameters for middle and end insertions and deletions.

2008-11-06 07:01  twu

	* src/stage1hr.c: Made fixes for splicing to work

2008-11-06 01:08  twu

	* src/indexdb_hr.h: Removed obsolete functions

2008-11-06 01:07  twu

	* src/indexdb_hr.c: Fixed masking of left shifts

2008-11-06 01:07  twu

	* src/indexdb.c: Commented out warning message for multiple index
	  files

2008-11-06 01:06  twu

	* src/gsnap.c: Partially implemented minlevel and maxlevel controls
	  for Stage1.  Removed references to Stage3chimera_T objects

2008-11-06 01:05  twu

	* src/: resulthr.c, resulthr.h: Removed references to
	  Stage3chimera_T objects

2008-11-06 01:04  twu

	* src/stage3hr.h: Implemented new structure for Stage3 objects:
	  single reads may have one or more substrings.

2008-11-06 01:04  twu

	* src/stage3hr.c: Implemented new structure for Stage3 objects:
	  single reads may have one or more substrings.  Modified print
	  procedure for indels to allow for mismatches.

2008-11-06 01:03  twu

	* src/stage1hr.h: Removed chimerap variable since Stage3 single
	  reads are all of the same type now.

2008-11-06 01:02  twu

	* src/stage1hr.c: Fixed polyat assessment at ends of query.
	  Storing first and last diagonals and computing mismatches on
	  both.  Changed ptr->indels to be consistently positive for
	  insertions and negative for deletions.  Using new Stage3 objects.
	  Solving middle indels with mismatches.  Using minlevel and
	  maxlevel to control computing behavior on different alignment
	  types.

2008-11-03 08:52  twu

	* src/stage1hr.h: Made max_insertions and max_deletions parameters.
	  Added minlevel and maxlevel.

2008-11-03 08:52  twu

	* src/stage1hr.c: Cleaned up procedures for single mismatches and
	  multiple mismatches.	Added oligobase to minus diagonals to
	  prevent negative coordinates.  Made max_insertions and
	  max_deletions parameters.  Added minlevel and maxlevel.

2008-10-28 08:42  twu

	* util/md_coords.pl.in: Revised instructions to user

2008-10-24 09:34  twu

	* src/stage3.c: In comparing paths_fwd and paths_rev, using just
	  number of matches

2008-10-24 09:34  twu

	* src/stage2.c: Also performing stage2 if there is a sufficient
	  value for ncoverage

2008-10-24 09:33  twu

	* src/stage1.c: Removed matchsize and matchinterval from Stage1_T
	  object, and allowing option in scan_ends of iterating on
	  different matchsizes.  In removal of repeated oligomers, now also
	  removing neighboring oligomers.  Now filtering gregions by
	  support.

2008-10-24 09:31  twu

	* src/reader.c: Added fields so Reader_reset_ends resets correctly

2008-10-24 09:30  twu

	* src/: gregion.c, gregion.h: Added function to filter by support

2008-10-24 09:29  twu

	* src/gmap.c: Fixed error message for -z flag

2008-10-24 09:29  twu

	* src/: diag.c, diag.h: Returning ncovered from
	  Diag_update_coverage

2008-10-24 09:29  twu

	* src/: block.c, block.h: Removed high-resolution option

2008-10-23 01:45  twu

	* src/stage3.c: Handling case where gap is at beginning of path.
	  Trimming end exons until a canonical intron is reached.

2008-10-23 01:44  twu

	* src/stage1.c: Identifying repeated oligos at the outset

2008-10-23 01:43  twu

	* src/pair.c: Made counting of ambiguous matches more uniform

2008-10-23 01:42  twu

	* src/gsnap-to-iit.c: Added information about unique positions.
	  Added ability to halt at a given position.

2008-10-23 01:41  twu

	* src/gregion.c: Modified print statement

2008-10-10 08:19  twu

	* src/pair.c: Made N's in query sequence align as mismatches in
	  GMAP.

2008-10-10 03:56  twu

	* src/gmapindex.c: Removing "chr" from chrsubset file

2008-10-10 03:55  twu

	* src/stage1hr.c: Tightened criteria for finding exon-exon
	  junctions.  Not reading 10- or 11-mers at ends if the 12-mer is
	  invalid.

2008-10-10 03:53  twu

	* src/stage3hr.c: Made macros for text constants

2008-10-10 03:52  twu

	* src/: match.c, match.h: Added function Match_print

2008-10-10 03:52  twu

	* src/gsnap.c: Changed default of trim flag to be false

2008-10-10 03:51  twu

	* src/gmap.c: Added jobdiv capability to GMAP

2008-10-01 23:50  twu

	* src/blackboard.c: Simplified the fix for the hang for input done
	  with no inputs

2008-10-01 05:20  twu

	* src/blackboard.c: Fixed hang that occurs when no input was ever
	  received, which happens with the jobdiv option when the input has
	  fewer sequences than the first batch modulus.

2008-09-26 06:00  twu

	* src/iit_get.c: Allowing retrieval of labels that contain colons,
	  by checking first to see if the first part of the label is a
	  divstring.

2008-09-26 05:59  twu

	* src/: iit-read.c, iit-read.h: Added function to determine divint
	  without reading entire IIT.

2008-09-23 10:44  twu

	* src/stage3.h: Added PRE_ENDS as a debugging endpoint

2008-09-23 10:43  twu

	* src/stage3.c: Modified solutions at ends.  First, we decide
	  between distal and medial, with distal penalized for
	  non-canonical introns.  Then, we simply extend the ends without
	  peelback and permitting an initial gap.

2008-09-23 10:41  twu

	* src/stage2.c: Introducing a minimum pct_coverage

2008-09-23 10:41  twu

	* src/: oligoindex.c, oligoindex.h: Allowed suffnconsecutive to be
	  a different value in each level of resolution.

2008-09-23 10:40  twu

	* src/: match.c, match.h: Moved function Match_get_coords to
	  gregion.c

2008-09-23 10:39  twu

	* src/gregion.h: Added fields for weight and support.

2008-09-23 10:39  twu

	* src/gregion.c: Added fields for weight and support.  Duplicate
	  gregions are now resolved in favor of the gregion with the
	  greatest weight, or if equal, the greatest support.

2008-09-23 10:37  twu

	* src/gmap.c: Increased extraband at end from 3 to 6

2008-09-23 10:36  twu

	* src/dynprog.c: Allowing a gap to start the alignment of end5 and
	  end3.  Introducing a parameter init_jump_penalty_p to control
	  this.

2008-09-23 10:34  twu

	* src/diag.c: Replaced 0 with 0U in some cases

2008-09-23 10:27  twu

	* src/stage1.c: Using weights on matches and on gregions to focus
	  on genomic regions with most specificity.

2008-09-19 03:49  twu

	* src/stage1.c: Added penalty for intron length in find_best_path
	  to reduce excessively large regions.	If segments are used, then
	  clearing gregions and starting over.

2008-09-16 08:50  twu

	* src/stage1hr.c: Fixed bug with false positives on middle indel.
	  Fixed bug with combinations of insertions and deletions in
	  find_segments_multiple_mm.

2008-09-15 04:01  twu

	* src/gmap.c: Allowing multiple paths for alignment against
	  user-provided segment.  Explicitly recomputing goodness over all
	  stage3 objects.  Allowing user to specify direction of introns.

2008-09-15 03:48  twu

	* src/stage2.c: Giving points for indexsize-equivalent number of
	  matches if it starts a new chain.

2008-09-15 03:46  twu

	* src/stage1hr.c: Fixed problem with insertions in first 12-mer.
	  Now treating as a mismatch, as we did for insertions in the last
	  12-mer.

2008-09-15 03:45  twu

	* src/oligoindex.h: Removed debug_graphic_p from argument list

2008-09-15 03:45  twu

	* src/oligoindex.c: Fixed memory leak

2008-09-15 03:44  twu

	* src/md5-compute.c: Added ability to handle multiple input files

2008-09-15 03:43  twu

	* src/: diag.c, diag.h, diagdef.h: Computing scores for each
	  diagonal and requiring a minimum score

2008-09-09 08:36  twu

	* src/stage1hr.c: Fixed bug in exact match to end of chromosome,
	  resulting in negative coordinates of the next chromosome.

2008-09-09 08:10  twu

	* src/stage3.h: Added function for recomputing goodness

2008-09-09 08:09  twu

	* src/stage3.c: Made widebandp true on all single gap solutions.
	  Extending 5' and 3' ends, rather than comparing distal with
	  medial, when defect rate is high.  Recomputing goodness using
	  just matches if best hit is poor.

2008-09-08 03:08  twu

	* src/: diag.c, diag.h: Moved some functions from oligoindex.c to
	  diag.c

2008-09-08 03:07  twu

	* src/: oligoindex.c, oligoindex.h: Implemented different mapping
	  resolutions by using multiple oligoindices.  Using a separate
	  lookback for each resolution.

2008-09-08 03:05  twu

	* src/: stage2.c, stage2.h: Implemented different mapping
	  resolutions by using multiple oligoindices.

2008-09-04 07:52  twu

	* configure.ac: Added check for stat64

2008-09-04 07:52  twu

	* acinclude.m4: Including config/acx_mmap_fixed.m4,
	  config/acx_mmap_variable.m4, and config/struct-stat64.m4.

2008-09-04 07:51  twu

	* VERSION: Updated version

2008-09-04 07:51  twu

	* README: Augmented instructions for new gmap_setup flags and made
	  mention of GSNAP.

2008-09-04 07:47  twu

	* src/: dynprog.c, dynprog.h: New functions added for dealing with
	  an internal gap

2008-09-04 07:47  twu

	* src/indexdb.c: Fixed problem in reading offsets and positions
	  file based on interval of 6.

2008-09-04 07:46  twu

	* src/gmap.c: Made default canonical mode to be 1

2008-09-04 06:37  twu

	* src/stage3.c: Reverted to revision 1.300 with newer code kept for
	  stage3debug.

2008-09-04 06:36  twu

	* src/stage2.c: Reverted to revision 1.221 with newer code kept for
	  converting oligomers to nucleotides

2008-09-04 06:32  twu

	* src/smooth.h: Removed stage2_indexsize

2008-09-04 06:31  twu

	* src/smooth.c: Reverted to revision 1.41, plus removal of
	  stage2_indexsize

2008-09-04 06:31  twu

	* src/oligoindex.h: Reverted to revision 1.47, plus most recent
	  wobble masking and code for multiple oligoindices

2008-09-04 06:29  twu

	* src/oligoindex.c: Reverted to revision 1.108, plus most recent
	  wobble masking and code for multiple oligoindices

2008-09-04 06:27  twu

	* src/diagpool.c: Removed initialization for bestscore and prev
	  fields

2008-09-04 06:26  twu

	* src/diagdef.h: Removed score, bestscore, and prev fields

2008-09-04 06:26  twu

	* src/diag.h: Reverted to revision 1.5 with some functions moved
	  from oligoindex.c.

2008-09-04 06:25  twu

	* src/diag.c: Reverted to revision 1.7 with some functions moved
	  from oligoindex.c.

2008-09-04 00:34  twu

	* src/stage3.h: Calling stage 2 directly

2008-09-04 00:33  twu

	* src/stage3.c: More attempts to rearrange steps

2008-09-04 00:32  twu

	* src/: stage2.c, stage2.h: Bypasses former stage 2 and returns
	  best path of diagonals, converted to nucleotides

2008-09-04 00:30  twu

	* src/smooth.c: Changed function for finding internal shorts

2008-09-04 00:29  twu

	* src/: oligoindex.c, oligoindex.h: Changed Oligoindex_get_mappings
	  to return a list of diagonals

2008-09-04 00:26  twu

	* src/iit-read.h: Added comments to explain arguments

2008-09-04 00:26  twu

	* src/gmap.c: Having stage2 return a path

2008-09-04 00:24  twu

	* src/diagpool.c: Added initialization for bestscore and prev

2008-09-04 00:22  twu

	* src/diagdef.h: Added fields for bestscore and prev

2008-09-04 00:22  twu

	* src/: diag.c, diag.h: Added functions Diag_compare_querystart and
	  Diag_best_path

2008-08-15 10:38  twu

	* src/: stage2.c, stage2.h, diag.c, diag.h, gmap.c, oligoindex.c,
	  oligoindex.h: Implementation of oligoindex step at multiple
	  resolutions

2008-08-15 06:40  twu

	* src/stage2.c: Rearranged procedures in preparation for multiple
	  oligoindices.

2008-08-15 06:39  twu

	* src/: oligoindex.c, oligoindex.h: Moved various functions from
	  oligoindex.c to diag.c.  Added various variables to Oligoindex_T
	  struct.  Rearranged procedures in preparation for multiple
	  oligoindices.

2008-08-15 06:38  twu

	* src/: diag.c, diag.h: Moved various functions from oligoindex.c
	  to diag.c

2008-08-15 02:47  twu

	* src/stage2.h: Added a version of stage 2 that can be called from
	  within stage 3.

2008-08-15 02:47  twu

	* src/stage2.c: Using active hits, instead of minactive and
	  maxactive bounds.  Added hooks for relying upon splice site
	  scores.  Made conversion to nucleotides handle arbitrary masks.
	  Added penalty for diffdistance not a multiple of 3.  Added a
	  version of stage 2 that can be called from within stage 3.

2008-08-15 02:44  twu

	* src/stage1hr.c: Exiting if a single polyat 12-mer found, to
	  prevent false indels from being found in
	  find_segments_multiple_mm.

2008-08-15 02:42  twu

	* src/oligoindex.h: Computing active hits around each diagonal,
	  instead of minactive and maxactive bounds.

2008-08-15 02:41  twu

	* src/oligoindex.c: Added wobble masking.  Computing dominance by
	  using scores, based on number of diagonals overlapping each
	  querypos.

2008-08-15 02:40  twu

	* src/indexdb_hr.c: Added masking for all left shifts

2008-08-15 02:39  twu

	* src/indexdb.c: Fixed problem where highest resolution indexdb was
	  not being used

2008-08-15 02:39  twu

	* src/gmap.c: Using new interface to Oligoindex_set_inquery

2008-08-15 02:37  twu

	* src/: diag.c, diag.h, diagdef.h: Added score to Diag_T object

2008-08-15 02:37  twu

	* src/block.c: Added error message

2008-08-11 04:15  twu

	* src/: oligoindex.c, oligoindex.h: Passing character strings to
	  procedures, rather than Sequence_T objects.

2008-08-10 03:38  twu

	* src/gmap.c: Made changes to debug requests from stage3

2008-08-09 14:12  twu

	* src/stage3.c: Rearranging steps to improve cross-species
	  performance.	Work still in progress.

2008-08-07 22:25  twu

	* src/stage1hr.c: Removed old code

2008-08-07 22:23  twu

	* src/stage1.c: Made heap and segment algorithm work for PMAP

2008-08-07 22:21  twu

	* src/: binarray.c, binarray.h: Removed binarray source code

2008-08-07 22:21  twu

	* src/sequence.c: Redefined trim_end for PMAP to exclude the
	  terminal stop codon added

2008-08-07 22:20  twu

	* src/pmapindex.c: Including index1interval in filename for PMAP
	  databases

2008-08-07 22:19  twu

	* src/matchpool.c: Removed old code that referred to positions, not
	  diagonals

2008-08-07 22:18  twu

	* src/match.c: Simplified a procedure

2008-08-07 22:18  twu

	* src/indexdbdef.h: For PMAP, allowed index1interval to be
	  determined by available databases

2008-08-07 22:17  twu

	* src/: indexdb_hr.c, indexdb_hr.h: Moved Indexdb_read_no_subst
	  command to indexdb.c

2008-08-07 22:16  twu

	* src/: indexdb.c, indexdb.h: Moved Indexdb_read_no_subst command
	  here.  Including index1interval into filename for PMAP databases.

2008-08-07 22:16  twu

	* src/gmap.c: Changed variable name from samplingp to lowidentityp

2008-08-07 22:15  twu

	* src/block.c: Bypassing oligo.c and calling Indexdb commands
	  directly

2008-08-06 07:13  twu

	* src/: Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am, Makefile.pmaptoo.am, stage1.c, stage1.h:
	  Removed binarray

2008-08-05 05:56  twu

	* src/: binarray.c, binarray.h, stage1.c: Transitioning away from
	  bins and toward segments.  Intermediate code contains both sets
	  of functions.

2008-08-01 03:50  twu

	* src/: block.c, block.h, gregion.c, gregion.h, matchpool.c,
	  matchpool.h, stage1.c: Just before change to using diagonals,
	  with directives indicating changes

2008-07-30 11:03  twu

	* src/gsnap.c: Changed batch specification so it runs from 0 to
	  n-1.

2008-07-30 10:51  twu

	* src/stage1hr.c: Changed hierarchy of results to be exact, sub:1,
	  local splicing, half introns, sub:2, sub:3, sub:4, indels,
	  distant splicing.  Increased speed for computing splice ends.
	  Limiting nmismatches for each splice end, so not checking
	  nmismatches for splicing after that.

2008-07-30 10:49  twu

	* src/gsnap.c: Reduced default maxpaths to 20 and maxchimerapaths
	  to 2

2008-07-29 10:46  twu

	* src/stage1hr.c: Improved identification of repetitive oligos

2008-07-29 10:45  twu

	* src/sequence.c: Better handling of FASTA files that end with
	  blank lines

2008-07-29 07:55  twu

	* src/: stage1hr.c, stage1hr.h: Implemented different sizes for
	  insertions and deletions

2008-07-29 05:56  twu

	* src/: stage3hr.c, stage3hr.h: Added function
	  Stage3_remove_duplicates

2008-07-29 05:56  twu

	* src/stage1hr.c: Made 12-mer mod 3 strategy work for multiple
	  mismatches, indels, and exon-exon junctions.

2008-07-28 10:08  twu

	* src/stage1hr.c: Removed special variables for -2, -1, querypos+1,
	  and querypos+2.  Removed middle_indel_p.

2008-07-28 08:49  twu

	* src/stage1hr.c: Made paired reads use new 12-mer strategy for
	  exact and 1-sub

2008-07-28 08:48  twu

	* src/stage1hr.h: Changed variable name to expected_pairlength

2008-07-28 08:48  twu

	* src/datadir.c: Improved error message when genome db not found

2008-07-28 03:33  twu

	* src/: intlist.h, stage1hr.c, indexdb_hr.c, indexdb_hr.h,
	  intlist.c: Implemented faster version of exact and 1-sub using
	  12-mers

2008-07-26 03:03  twu

	* src/indexdb_hr.c: Removed oligo_hr.h and oligo_hr.c.	Added code
	  for reading left and right subst of 1 and 2 nts.

2008-07-26 03:02  twu

	* src/: oligo_hr.c, oligo_hr.h: Removed oligo_hr.h and oligo_hr.c

2008-07-26 03:02  twu

	* src/: stage1hr.c, Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am, Makefile.pmaptoo.am, block.c, indexdb.c,
	  indexdb.h: Removed oligo_hr.h and oligo_hr.c.

2008-07-26 03:02  twu

	* src/indexdb_hr.h: Initial import into CVS

2008-07-17 11:02  twu

	* src/stage3hr.c: Fixed handling of trimming for inverted hits.
	  Fixed handling of hits that have negative genomic coordinates.

2008-07-17 11:02  twu

	* src/stage1hr.c: Fixed handling of trimming at ends

2008-07-17 11:01  twu

	* src/pair.c: Changed output to show "genome" instead of "chr"

2008-07-17 11:00  twu

	* src/: Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am, Makefile.pmaptoo.am, diagnostic.c,
	  diagnostic.h, gmap.c, result.c, result.h, stage1.c, stage1.h:
	  Added Diagnostic_T to hold information

2008-07-17 10:59  twu

	* src/: chimera.c, chimera.h, get-genome.c, iit_plot.c, match.c,
	  match.h, stage3.c: Using new interface to Genome_get_segment

2008-07-17 10:57  twu

	* src/: genome.c, genome.h: Printing out-of-bounds characters on
	  all cases where coordinates exceed chromosomal boundaries.

2008-07-07 06:46  twu

	* src/stage1hr.c: Added comment

2008-07-07 06:46  twu

	* src/stage1.c: Added high-resolution sampling

2008-07-07 06:45  twu

	* src/: oligo.c, oligo.h: Removed burden of leftreadshift to caller

2008-07-07 06:45  twu

	* src/: indexdb.c, indexdb.h: Added function to provide indexing
	  interval

2008-07-07 06:44  twu

	* src/: block.c, block.h: Added high-resolution behavior to Block_T
	  object

2008-07-07 06:43  twu

	* src/gmap.c: Added hybrid behavior for finding canonical introns:
	  low reward for high-identity sequences and high reward otherwise.

2008-07-07 05:02  twu

	* src/stage1.h: Removed obsolete functions

2008-07-07 05:02  twu

	* src/stage1.c: Renamed variables

2008-07-07 02:26  twu

	* src/stage2.h: Computing separate runtimes for stage2
	  diagonalization and alignment.

2008-07-07 02:25  twu

	* src/stage2.c: Reinstating limitation on maximum number of active
	  hits.  Computing separate runtimes for stage2 diagonalization and
	  alignment.

2008-07-07 02:24  twu

	* src/: stage1.c, stage1.h: Reporting whether sampling was used

2008-07-07 02:24  twu

	* src/: pair.c, pair.h, stage3.c: Printing separate runtimes for
	  stage2 diagonalization and alignment

2008-07-07 02:23  twu

	* src/gmap.c: Using smaller stage 2 indexsize when stage 1 sampling
	  is done

2008-07-07 00:09  twu

	* src/: plotgenes.c, plotgenes.h: Added ability to handle values

2008-07-07 00:09  twu

	* src/pdldata.c: Using Access_mmap function

2008-07-07 00:08  twu

	* src/: gdiag.c, gsnap-to-iit.c: Using new interface to
	  Genome_fill_buffer

2008-07-07 00:07  twu

	* src/subseq.c: Added initial '>' to header

2008-07-07 00:07  twu

	* src/stage3.c: Using new interface to IIT_print

2008-07-07 00:07  twu

	* src/stage1.c: Removed references to Matchpair_T

2008-07-07 00:06  twu

	* src/pmapindex.c: Removed -l as an input flag

2008-07-07 00:04  twu

	* src/: oligo.c, oligo.h: Added code for identifying repetitive
	  oligos

2008-07-07 00:03  twu

	* src/: match.c, match.h: Added code for dealing with pairs of
	  matches

2008-07-07 00:03  twu

	* src/: matchpair.c, matchpair.h: Removed Matchpair_T code

2008-07-07 00:02  twu

	* src/indexdb.h: Restoring previous definition of sufficient
	  support

2008-07-07 00:01  twu

	* src/iit_update.c: Using new interface to IIT_read

2008-07-07 00:01  twu

	* src/iit_plot.c: Handling values, in addition to counts and genes

2008-07-07 00:00  twu

	* src/: gregion.c, gregion.h: Added fields to Gregion_T

2008-07-06 23:59  twu

	* src/gmap.c: Interpreting optarg as strings, not integers

2008-07-06 23:58  twu

	* src/get-genome.c: Removed -F and -R flags.  Using -R flag for
	  relative coordinates.

2008-07-06 23:57  twu

	* src/block.h: Separated interfaces for GMAP and PMAP

2008-07-06 23:57  twu

	* src/block.c: Added hook for removing repetitive oligos

2008-07-06 23:57  twu

	* src/binarray.c: Taking all boxes in final step.  Reduced
	  debugging output.

2008-07-06 23:55  twu

	* src/: Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am, Makefile.pmaptoo.am: Added binarray.c and
	  .h and removed matchpair.c and .h

2008-07-06 23:52  twu

	* src/matchpair.c: Added code for bins

2008-07-06 23:49  twu

	* src/stage1.c: Added two levels of ntopboxes

2008-07-03 08:25  twu

	* src/: binarray.c, binarray.h, stage1.c: Implemented working
	  version of binarray algorithm

2008-07-03 05:20  twu

	* src/: revcomp.c, seqlength.c, subseq.c, Makefile.util.am: Added
	  utility programs for internal use

2008-07-02 11:29  twu

	* src/: binarray.c, binarray.h: Initial import into CVS

2008-07-01 04:10  twu

	* src/: stage1.c, stage1.h: Initial implementation of bins

2008-06-30 00:05  twu

	* src/stage3.c: Added ability to print relative coordinates

2008-06-30 00:04  twu

	* src/stage1hr.c: Improved handling of heaps.  Added code for
	  handling out-of-bounds conditions.

2008-06-30 00:03  twu

	* src/: sequence.c, sequence.h: Added command for printing revcomp
	  of sequence

2008-06-30 00:03  twu

	* src/interval.c: Added debugging statements

2008-06-30 00:02  twu

	* src/indexdb_hr.c: Replaced separate variables for heapsize and
	  delta into a single header.  Added code for doing all reads, then
	  doing all writes.

2008-06-29 23:54  twu

	* src/indexdb.c: Added debugging statements

2008-06-29 23:54  twu

	* src/iitdef.h: Storing separate mmap pointers for parts of IIT

2008-06-29 23:53  twu

	* src/: iit-read.c, iit-read.h: Added ability to print relative
	  coordinates

2008-06-29 23:53  twu

	* src/gmap.c: Removed -R flag

2008-06-29 23:52  twu

	* src/gsnap.c: Added ability to handle input sequence in batches

2008-06-29 23:45  twu

	* src/: genome.c, genome.h: Changed out-of-bounds symbol to be '*'.

2008-06-25 03:24  twu

	* src/gmap.c: Made low reward for canonical sequences to be the
	  default

2008-06-25 03:17  twu

	* src/get-genome.c: Fixed calculation of genomiclength

2008-06-25 03:16  twu

	* src/iit-read.h: Removed unused function.

2008-06-25 03:16  twu

	* src/iit-read.c: Now doing memory mapping of pointers rather than
	  reading all of them.	Fixed bug in reporting second chromosomal
	  coordinate.  Fixed bug in sorting segments by coordinate.

2008-05-19 11:12  twu

	* src/indexdb_hr.c: Made process_heap inline.  Removed delta from
	  Batch_T.

2008-05-19 07:46  twu

	* src/indexdb_hr.c: Various code introduced to improve speed of
	  heapify operation

2008-05-09 02:33  twu

	* src/: access.c, access.h: Fixed mmap calls with offset so offset
	  is on a page boundary

2008-05-09 02:31  twu

	* src/: stage3hr.c, stage3hr.h: Added new functions for filtering
	  and sorting chimeras.  Fixed calls of scrambled exons.

2008-05-09 02:30  twu

	* src/stage1hr.c: Major efficiency improvements in heapify and
	  other heap functions for merging diagonals

2008-05-09 02:30  twu

	* src/indexdb_hr.c: Major efficiency improvements in heapify and
	  other heap functions for merging batches

2008-05-08 20:11  twu

	* src/stage1hr.c: Changed filtering methodology for exon-exon
	  junctions

2008-05-08 14:22  twu

	* src/indexdb_hr.c: Using pointers to memory-mapped positions file,
	  and adding shift-plus-diagterm as heap builds the final array of
	  positions.

2008-05-07 05:30  twu

	* src/indexdb_hr.c: Restored previous version

2008-05-07 05:29  twu

	* src/indexdb_hr.c: Attempt to reduce D2 cache miss rate, but
	  actually increases it by 10x.

2008-05-06 02:15  twu

	* src/stage3hr.c: Using correct type for Stage3chimera_t objects

2008-05-06 02:15  twu

	* src/stage1hr.c: Set chimerap flag correctly

2008-05-06 02:14  twu

	* src/indexdb_hr.c: Faster counting of entries in cases where
	  duplicates are not allowed

2008-05-06 02:13  twu

	* src/indexdb.c: Minor syntactic changes

2008-05-06 01:42  twu

	* src/gsnap.c: Turned off reading of labels for map iit files

2008-05-05 07:35  twu

	* src/: gmapindex.c, pmapindex.c: Providing chromosome_iit to
	  procedures for writing offset and position files

2008-05-05 07:34  twu

	* src/: stage3hr.c, stage3hr.h: Values for chrnum are pre-computed
	  rather than computed here

2008-05-05 07:34  twu

	* src/stage1hr.c: Using new interfaces to Genome_fill_buffer and
	  Stage3_new routines

2008-05-05 07:33  twu

	* src/: indexdb.c, indexdb.h: No longer storing oligomers at ends
	  of chromosomes

2008-05-05 07:32  twu

	* src/: iit-read.c, iit-read.h, iitdef.h: Providing specific fields
	  for memory mapping of labels and annotations.  Reading all
	  pointers for labels and annotations.

2008-05-05 07:30  twu

	* src/: genome.c, genome.h: Trimming correctly at chromosome
	  boundaries.  Returning chrnum.

2008-05-05 07:30  twu

	* src/access.h: Added function to mmap at a particular offset.

2008-05-05 07:30  twu

	* src/access.c: Added function to mmap at a particular offset.
	  Added check for struct stat64.

2008-05-05 02:50  twu

	* src/stage1hr.c: Searching for indels only if substitution fails

2008-05-04 12:11  twu

	* src/: stage1hr.c, stage1hr.h, stage3hr.c, stage3hr.h, gsnap.c:
	  Added trimming of mismatches at ends of substitutions

2008-04-25 05:46  twu

	* src/: stage3hr.c, stage3hr.h: Printing information about paired
	  result type and about structural variations in spliced reads.

2008-04-25 05:46  twu

	* src/stage3.c: Removed include of maxent.h

2008-04-25 05:45  twu

	* src/: stage1hr.c, stage1hr.h: Added hierarchy of paired result
	  types.  Checking for cross repetitiveness.

2008-04-25 05:42  twu

	* src/sequence.c: Improved debugging statements

2008-04-25 05:42  twu

	* src/: resulthr.c, resulthr.h: Storing information about paired
	  result type

2008-04-25 05:41  twu

	* src/pair.c: Changed output format for IIT-readable files (-f 7)

2008-04-25 05:40  twu

	* src/: list.c, list.h: Added function of List_to_array that
	  reports list length

2008-04-25 05:39  twu

	* src/: iit_plot.c, plotgenes.c, plotgenes.h: Fixed handling of new
	  IIT map format

2008-04-25 05:36  twu

	* src/iit-read.c: Fixed handling of flanking intervals

2008-04-25 05:35  twu

	* src/gsnap.c: Adding information about paired result type and
	  providing information about max number of paired paths.

2008-04-25 05:34  twu

	* src/Makefile.gsnaptoo.am: Using tables for IITs.  Removed
	  iit_update.

2008-04-25 05:31  twu

	* src/Makefile.dna.am: Using tables for IIT.  Removing gdiag and
	  iit_update.

2008-04-23 10:27  twu

	* src/iit_get.c: Fixed bug in handling queries from stdin

2008-04-22 07:17  twu

	* src/stage3hr.c: Slight improvement in efficiency in eliminating
	  duplicates or dominated paired end solutions.

2008-04-22 07:10  twu

	* src/dynprog.c: Reduced mismatch penalty for low quality
	  sequences.  Equalizing extension penalty for single gaps,
	  regardless of sequence quality.

2008-04-22 07:07  twu

	* src/maxent.c: Added debugging statements

2008-04-22 07:06  twu

	* src/stage3hr.c: Fixed bugs in eliminating duplicate or dominated
	  paired-end results

2008-04-22 07:05  twu

	* src/iit-read.c: Fixed memory leak for entire IIT structure

2008-04-22 06:40  twu

	* src/stage3.c: In dual break, peeling pairs first.

2008-04-22 05:31  twu

	* src/stage3.c: Improved handling of dual breaks by scanning
	  genomic segment

2008-04-21 04:05  twu

	* src/iit_store.c: Fixed bug in handling intervals without divs

2008-04-21 04:04  twu

	* src/iit-write.c: Added error message if total_nintervals is zero.

2008-04-21 04:04  twu

	* src/iit-read.c: Modified output for IIT_dump

2008-04-21 04:03  twu

	* tests/: fa.iittest, iit_get.out.ok: Modified IIT input/output for
	  new interval format

2008-04-21 02:17  twu

	* src/: stage3hr.c, stage3hr.h: Added code for printing half
	  introns.  Now storing chrnum when Stage3_T objects are computed.
	  Using chrnum to determine whether two paired ends are
	  connectable.

2008-04-21 02:16  twu

	* src/stage1hr.c: Using scores to determine whether indel beats
	  substitution.  Added code for finding half introns.  Now storing
	  chrnum when Stage3_T objects are computed.

2008-04-21 02:14  twu

	* src/indexdb_hr.c: Added code, not currently used, for using
	  doubles to find longer oligomers.

2008-04-15 06:03  twu

	* src/: stage1hr.c, stage1hr.h: Increased MAX_INDELS, and using it
	  instead of hard-coded 3

2008-04-15 06:01  twu

	* src/: table.c, table.h: Added functions Table_string_compare and
	  Table_string_hash

2008-04-15 06:00  twu

	* src/pmapindex.c: Using new interface to IIT_read

2008-04-15 06:00  twu

	* src/: plotgenes.c, plotgenes.h, stage3.c: Using new interface to
	  IIT_get and IIT_label

2008-04-15 05:59  twu

	* src/: plotdata.c, segmentpos.c, stage3hr.c: Using new interface
	  to IIT_label

2008-04-15 05:59  twu

	* src/: match.c, pair.c: Using new interface to Chrnum_to_string

2008-04-15 05:58  twu

	* src/indexdb.c: Using IIT_total_nintervals

2008-04-15 05:56  twu

	* src/indexdbdef.h: Moved definition of Indexdb_T to a separate
	  file

2008-04-15 05:55  twu

	* src/iitdef.h: Added fields for whether labels were read, and for
	  offsets to various parts of the iit file.

2008-04-15 05:41  twu

	* src/iit_store.c: Using new version for reporting intervals

2008-04-15 05:40  twu

	* src/iit_get.c: Using new interface to IIT_get and IIT_read.
	  Added ability to center annotations at a given column.

2008-04-15 05:37  twu

	* src/: iit_dump.c, iit_plot.c: Using new interface to IIT_read

2008-04-15 05:37  twu

	* src/iit-write.c: Fixed bugs for divs with no intervals

2008-04-15 05:36  twu

	* src/: iit-print.c, iit-print.h: Moved IIT_print procedures back
	  to iit-read.c.

2008-04-15 05:35  twu

	* src/: iit-read.c, iit-read.h: Fixed bug in handling divs with no
	  intervals.  Allowing memory mapping of labels and intervals and
	  their pointers (in addition to annotations).	Moved IIT_print
	  procedures back to this file.

2008-04-15 05:33  twu

	* src/gsnap.c: Providing flag for user to specify consecutive
	  matches, to control speed

2008-04-15 05:30  twu

	* src/gsnap-to-iit.c: Removed flag for old GSNAP version output
	  format

2008-04-15 05:29  twu

	* src/gmapindex.c: Using tables to provide information to IIT_write

2008-04-15 05:26  twu

	* src/: get-genome.c, gmap.c: Using new interface to IIT_get and
	  IIT_read

2008-04-15 05:25  twu

	* src/genome-write.c: Using new interface to IIT_get

2008-04-15 05:23  twu

	* src/: chrnum.c, chrnum.h, chrsubset.c, gdiag.c, genomepage.c,
	  genomeplot.c: Using new interface to IIT_label

2008-04-10 07:55  twu

	* src/: gregion.c, match.c, matchpool.c: Made IIT_get_one pass
	  additional parameter

2008-04-01 05:18  twu

	* src/stage1hr.c: Various methods to improve speed, including
	  separate processing for plus and minus strands, use of
	  threshold_noligomers and a user-specified threshold_score for
	  finding segments for multiple mismatches.

2008-03-31 10:26  twu

	* src/stage1hr.c: Removed old code based on fixed (nonrecursive)
	  oligosize

2008-03-31 10:10  twu

	* src/stage1hr.h: Changed variable names

2008-03-31 10:10  twu

	* src/stage1hr.c: Using new variable names for paired-end lengths.
	  Generalized mask for oligosize.

2008-03-31 10:04  twu

	* src/gsnap.c: Removed -a flag and replaced it with -S flag.
	  Changed flags for paired-end lengths.

2008-03-31 09:52  twu

	* src/segmentpos.c: Using new interface to IIT routines with divs.

2008-03-31 09:50  twu

	* src/get-genome.c: Moved Chrom_string_from_position function to
	  iit-print.c

2008-03-31 09:49  twu

	* src/: chrnum.c, chrom.c, chrom.h, chrsubset.c: Using new
	  interface to IIT routines with divs.

2008-03-31 09:47  twu

	* src/stage3hr.h: Changed variable names for paired-end lengths.

2008-03-31 09:47  twu

	* src/stage3hr.c: Using new interface to IIT routines wiht divs.
	  Changed variable names for paired-end lengths.

2008-03-31 06:38  twu

	* src/stage1hr.c: Made indel alignments extend inward from ends as
	  far as possible.

2008-03-31 02:09  twu

	* src/stage1hr.c: Added new routine for computing indels without
	  using dynamic programming matrix.  Maximizes matches from left to
	  right.

2008-03-27 06:43  twu

	* src/: iit-read.h, iit-write.c, iit-write.h, iit_get.c,
	  iit_store.c, iitdef.h, iit-print.c, iit-print.h, iit-read.c:
	  Introduced version 3 of IIT format, to handle multiple divs.

2008-03-20 03:52  twu

	* src/: Makefile.dna.am, Makefile.gsnaptoo.am: Removed block_hr and
	  blockdef files

2008-03-20 03:50  twu

	* src/pmapindex.c: Removed both uppercase and lowercase flags, and
	  added -l flag to make the distinction

2008-03-20 03:48  twu

	* src/stage3hr.c: Changed order of output so type of match comes
	  before genomic location

2008-03-20 03:46  twu

	* src/stage1hr.c: Handling short reads with lowercase characters.
	  Using Oligo_hr functions rather than Block_T functions.

2008-03-20 03:42  twu

	* src/: sequence.c, sequence.h: Added functions to handle short
	  reads with lowercase characters

2008-03-20 03:40  twu

	* src/: oligo_hr.c, oligo_hr.h: Moved leftreadshift step out of
	  oligo_hr functions

2008-03-20 03:09  twu

	* src/oligo-count.c: Using new interface to Block_new

2008-03-20 03:08  twu

	* src/indexdb_hr.c: Removed checking for duplicates

2008-03-20 03:08  twu

	* src/: indexdb.c, indexdb.h: Added ability to mask lowercase
	  characters in genome

2008-03-20 03:07  twu

	* src/gsnap.c: Made program work for query sequences with lower
	  case

2008-03-20 03:06  twu

	* src/gmapindex.c: Removed uppercase and lowercase flags and added
	  -l flag.  Making ".masked" indexdb files for masked genomes
	  (where lowercase nts not indexed).

2008-03-20 02:58  twu

	* src/: genome.c, genome.h: Changed name of variable

2008-03-20 02:56  twu

	* src/: block.c, block_hr.c, block_hr.h, blockdef.h: Restored
	  definition of Block_T to block.c

2008-03-05 15:09  twu

	* src/gsnap.c: Using new interfaces to Stage1 procedures

2008-03-05 15:08  twu

	* src/stage1hr.c: Deleted debugging statements that give a seg
	  fault

2008-03-05 15:06  twu

	* src/: stage1hr.c, stage1hr.h: Generalized procedures to use
	  arbitrary oligosize

2008-03-05 15:00  twu

	* src/stage1.c: Using new interface to Block_new

2008-03-05 14:59  twu

	* src/indexdb_hr.c: Fixed bugs in adding wildcard nucleotides

2008-03-05 14:58  twu

	* src/indexdb.c: Fixed bug in recognizing index file at interval 6

2008-03-05 14:57  twu

	* src/: block.c, block.h, block_hr.c, blockdef.h, oligo.c, oligo.h,
	  oligo_hr.c, oligo_hr.h: Generalized procedures to handle
	  arbitrary oligosize

2008-03-05 08:22  twu

	* src/: Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am: Added new source files

2008-03-05 08:21  twu

	* src/stage3hr.c: Generalized print procedures to handle
	  arbitrarily long reads

2008-03-05 08:21  twu

	* src/: stage1hr.c, stage1hr.h: Added recursive procedures for
	  paired end reads

2008-03-05 08:19  twu

	* src/stage1.c: Using original GMAP calls to Block_T procedures

2008-03-05 08:18  twu

	* src/: oligo.c, oligo.h, oligo_hr.c, oligo_hr.h: Moved
	  GSNAP-specific procedures to a separate file

2008-03-05 08:18  twu

	* src/: intlist.c, intlist.h: Added function
	  Intlist_ascending_by_key

2008-03-05 08:17  twu

	* src/indexdb_hr.c: Moved GSNAP-specific procedures to a separate
	  file.

2008-03-05 08:17  twu

	* src/indexdb.h: Using "id<number>" as file suffix for offsets and
	  positions files.

2008-03-05 08:16  twu

	* src/indexdb.c: Moved definition of Indexdb_T object to a separate
	  file.  Separated GSNAP-specific procedures to a separate file.
	  Using "id<number>" as file suffix for offsets and positions
	  files.

2008-03-05 08:11  twu

	* src/gmapindex.c: Removed -e flag for specifying subindexing

2008-03-05 08:10  twu

	* src/: block_hr.c, block_hr.h: Made separate file for
	  GSNAP-specific procedures

2008-03-05 08:09  twu

	* src/blockdef.h: Put Block_T definition into a separate file

2008-03-05 08:09  twu

	* src/block.h: Removed Block_T procedures specific to GSNAP

2008-03-05 08:08  twu

	* src/block.c: Put Block_T definition into a separate file.
	  Removed GSNAP parameters for GMAP calls to Block_T procedures.

2008-03-04 02:02  twu

	* src/stage1hr.c: Implemented recursive method for finding exact
	  matches.  Binary search not yet added.

2008-03-03 04:37  twu

	* Makefile.am, cvs2cl.pl: Made maintainer Perl machine-independent

2008-03-03 04:35  twu

	* util/: fa_coords.pl.in, gmap_process.pl.in, gmap_setup.pl.in,
	  md_coords.pl.in: Made different make commands for gmapdb_highres
	  and gmapdb_lowres

2008-03-03 04:34  twu

	* src/: Makefile.dna.am, Makefile.gmaponly.am,
	  Makefile.gsnaptoo.am: Customized each Makefile.am for its
	  specific task

2008-02-29 05:39  twu

	* src/: gmapindex.c, iit-read.c, segmentpos.c: Using new interface
	  to obtain strings from Chrom_T objects

2008-02-29 05:37  twu

	* src/: chrom.c, chrom.h: Restricted criteria for considering
	  initial part of chromosome string as numeric.  Now storing
	  initial string directly.

2008-02-29 03:29  twu

	* src/gsnap.c: Using new interface to print commands

2008-02-28 15:17  twu

	* src/: stage3hr.c, stage3hr.h: Changed output to be more uniform,
	  in a 1-column format

2008-02-28 02:23  twu

	* src/list.c: Added include of string.h

2008-02-28 02:22  twu

	* src/iit_plot.c: Made program able to print counts

2008-02-28 02:20  twu

	* src/iit-read.c: Added more informative error messages when offset
	  appears incorrect relative to filesize.  Removed output of type
	  in print_record.

2008-02-28 02:17  twu

	* src/gsnap-to-iit.c: Handles new GSNAP output format.	Handles
	  remapping to genome.

2008-02-28 02:17  twu

	* src/get-genome.c: Made program work correctly on chromosomally
	  tagged IIT map files

2008-02-28 02:15  twu

	* src/: genomepage.c, genomepage.h: Removed sequence as a parameter

2008-02-28 02:15  twu

	* src/: pair.c, pair.h, stage3.c: Modified output of exon map

2008-02-28 02:13  twu

	* src/: plotgenes.c, plotgenes.h: Added function for printing
	  counts

2008-02-28 02:12  twu

	* src/: Makefile.dna.am, Makefile.gsnaptoo.am, blackboard.c,
	  blackboard.h, gmap.c, gsnap.c, params.c, params.h, reqpost.c,
	  reqpost.h: Removed Params_T object

2008-02-26 06:40  twu

	* src/gsnap-to-iit.c: Handling new version of gsnap output (after
	  remapping).

2008-02-25 21:39  twu

	* src/gsnap-to-iit.c: Added -b flag to specify blocksize.  Made
	  default blocksize 10000.

2008-02-13 08:09  twu

	* src/: iit_plot.c, plotgenes.c, plotgenes.h: Fixed printing of
	  genes in ascii format

2008-02-08 00:53  twu

	* src/: plotgenes.c, plotgenes.h: Added binning by pixel.  Removed
	  allgenesp for plot_counts.

2008-02-07 06:12  twu

	* src/: gsnap-to-iit.c, plotgenes.c: Modified count format for IITs
	  to store information in batches

2008-02-07 05:17  twu

	* src/plotgenes.c: Added printing of alternate counts.	Fixed
	  problem for calls to IIT_get_typed.

2008-02-07 05:15  twu

	* src/gsnap-to-iit.c: Initial import into CVS

2008-02-06 04:14  twu

	* src/iit_plot.c: Increased top margin.  Added -V flag for handing
	  count data.

2008-02-06 04:12  twu

	* src/: plotgenes.c, plotgenes.h: Added function for plotting count
	  data.  Handling signs for both versions 1 and 2 of IIT files.

2008-02-06 04:11  twu

	* src/iit-read.h: Added interface for IIT_version()

2008-02-06 04:10  twu

	* src/iit-read.c: Added abort statement for negative coordinates

2008-02-06 04:05  twu

	* src/sequence.c: Added functions for skipping sequences

2008-02-06 04:04  twu

	* src/indexdb.c: Commented out some information output to stderr

2008-02-06 04:03  twu

	* src/iit_get.c: If iit file not found, try adding ".iit" suffix

2008-02-06 04:00  twu

	* src/stage3hr.c: Printing distances for spliced reads only if
	  distance value is nonzero

2008-02-06 03:59  twu

	* src/stage1hr.c: Fixed calculation of distances in spliced reads

2008-02-05 03:26  twu

	* src/: Makefile.gmaponly.am, Makefile.gsnaptoo.am,
	  Makefile.pmaptoo.am: Added compiler commands for iit_plot

2008-02-05 03:25  twu

	* src/iit_plot.c: Taken from mapplot.c in gdp.

2008-02-05 03:25  twu

	* src/: genomepage.c, genomepage.h: Extracted commands from
	  gdata-write in gdp.

2008-02-05 03:24  twu

	* src/: plotgenes.c, plotgenes.h: Incorporated changes from gdp.
	  Improved plotting capabilities.

2008-02-05 03:22  twu

	* src/: list.c, list.h: Incorporated changes from gdp.	Added
	  List_from_string.

2008-02-05 03:22  twu

	* src/color.c: Incorporated changes from gdp.  Removed yellow.

2008-01-30 02:27  twu

	* src/gsnap.c: Limited reporting of exon-exon paths.  Added -E flag
	  to turn off finding of exon-exon solutions.

2008-01-30 02:26  twu

	* src/: genome.c, genome.h: Made Genome_fill_buffer return a false
	  value if it goes into negative genome coordinates.

2008-01-29 10:16  twu

	* src/stage1hr.c: Skipping cases that result in negative genomic
	  coordinates.	Skipping cases of finding first indels when
	  alignment doesn't extend to the end.

2008-01-29 08:35  twu

	* src/: stage3hr.c, stage3hr.h: Made fixes for handling exon-exon
	  junctions

2008-01-29 08:05  twu

	* src/stage1hr.c: Fixed problems in handling various combinations
	  of sense/antisense and plus/minus strands for exon-exon
	  junctions.

2008-01-29 07:45  twu

	* src/gmap.c: Made finding canonical introns the default.  Made -X
	  flag take an argument.

2008-01-16 08:48  twu

	* src/: stage1hr.c, stage3hr.c, stage3hr.h: Improved algorithm for
	  finding and ranking chimeras

2008-01-14 08:49  twu

	* src/: gmap.c, pair.c, pair.h, stage3.c, stage3.h: Added output in
	  IIT exon map format

2008-01-14 08:02  twu

	* src/: stage1hr.c, stage3hr.c, stage3hr.h: Added printing of
	  number of mismatches for chimeras

2008-01-14 04:26  twu

	* src/dynprog.c: Added type cast for memset.

2008-01-14 04:25  twu

	* src/stage1hr.c: Reduced max mismatches to 4.	Penalized
	  mismatches further in finding breakpoints for chimeras.

2008-01-14 04:07  twu

	* src/stage3hr.c: Reporting breakpoint coordinates for chimeras

2008-01-14 02:00  twu

	* src/stage1hr.c: Increased penalty for mismatches to help find
	  correct breakpoint for chimeras

2008-01-11 09:00  twu

	* src/: Makefile.gmaponly.am, Makefile.gsnaptoo.am,
	  Makefile.pmaptoo.am, stage1hr.c, stage3hr.c, stage3hr.h: Added
	  probabilistic calculations of splice sites

2008-01-11 07:17  twu

	* src/: stage1hr.c, stage1hr.h, stage3hr.c, stage3hr.h, gsnap.c:
	  Implemented code for identifying chimeras

2008-01-11 07:16  twu

	* src/: resulthr.c, resulthr.h: Added a new type for chimeras

2008-01-09 07:47  twu

	* src/stage1hr.c: Fixed typo in variable name

2008-01-09 07:44  twu

	* src/: resulthr.c, resulthr.h, stage3hr.c, stage3hr.h: Added the
	  ability to report paired-end cases that fail to co-localize

2008-01-09 07:37  twu

	* src/gsnap.c: Added the ability to report paired-end cases that
	  fail to co-localize

2008-01-09 07:24  twu

	* src/gmap.c: Cleaned up some code

2008-01-09 02:03  twu

	* src/: gsnap.c, stage1hr.c, stage1hr.h: Added -o flag to specify
	  optimum length

2008-01-08 08:48  twu

	* src/gsnap.c: Added -I flag for specifying inversion of second
	  read of paired end read

2008-01-08 08:48  twu

	* src/: sequence.c, sequence.h: Added procedure for printing
	  revcomp of a short read

2008-01-08 08:40  twu

	* src/: stage3hr.c, stage3hr.h: Provided options for printing
	  second read either in original direction or as reverse
	  complement.

2008-01-08 08:39  twu

	* src/stage1hr.c: Fixed various memory leaks

2008-01-08 07:02  twu

	* src/gsnap.c: Added flag to print all solutions, either for single
	  read or for paired end read.

2008-01-08 06:46  twu

	* src/: stage3hr.c, stage3hr.h: Added procedures for sorting
	  results of single read mappings

2008-01-08 06:44  twu

	* src/: stage1hr.c, stage1hr.h: Added ability to print all
	  solutions in single read

2008-01-08 05:48  twu

	* src/: stage3hr.c, stage3hr.h: Added sorting of results by
	  closeness to optimal distance

2008-01-08 05:48  twu

	* src/gsnap.c: Removed unused variables.  Removed instant printing
	  feature.

2008-01-08 05:47  twu

	* src/: stage1hr.c, stage1hr.h: Removed instant printing feature

2008-01-07 09:44  twu

	* src/: resulthr.c, resulthr.h: Generalized Result_T object so it
	  can print either single or paired end results

2008-01-07 09:44  twu

	* src/: sequence.c, sequence.h: Implemented procedure for reading
	  short reads, either single or paired ends.

2008-01-07 09:43  twu

	* src/: request.c, request.h: Enabled storage of paired reads in
	  Request_T object

2008-01-07 09:42  twu

	* src/: stage3hr.c, stage3hr.h: Implemented routines for storing
	  and printing paired ends

2008-01-07 09:27  twu

	* src/stage1hr.c: Implemented separate strategy for handling reads
	  with poly-A or poly-T 12-mers.  In such cases, need to test
	  12-mers exhaustively.

2008-01-07 03:37  twu

	* src/: stage1hr.c, stage1hr.h: Initial implementation of mapping
	  for paired reads.  For consistency, changed indel to be same rank
	  as sub:2 for single reads.  Generalized separator used in
	  printing results.

2008-01-04 03:31  twu

	* src/stage1hr.c: Separated single read strategy into separate
	  components

2008-01-04 03:28  twu

	* src/sequence.c: Fixed a memory leak.

2008-01-04 01:22  twu

	* src/: stage3hr.c, stage3hr.h: Added a stage3 procedure specific
	  for GSNAP

2008-01-04 01:21  twu

	* src/: sequence.c, sequence.h: Added a read procedure that
	  converts input to uppercase

2008-01-04 01:19  twu

	* src/: gsnap.c, resulthr.c, resulthr.h: Made GSNAP algorithm
	  return results rather than printing them

2008-01-04 01:19  twu

	* src/: Makefile.gmaponly.am, Makefile.gsnaptoo.am,
	  Makefile.pmaptoo.am: Removed gregion.c and added stage3hr.c to
	  GSNAP build

2008-01-04 01:17  twu

	* src/: stage1hr.c, stage1hr.h: Made algorithm return results
	  rather than printing them.  Fixed a bug in handling cases with
	  mismatches on both ends.

2007-12-19 03:16  twu

	* src/: gmap.c, pair.c, pair.h, stage3.c, stage3.h: Added -4 flag
	  for printing alignments per exon

2007-12-19 03:11  twu

	* src/gsnap.c: Removed unused code

2007-12-19 03:05  twu

	* src/stage1hr.c: Removed unused header files and objects

2007-12-19 03:04  twu

	* src/: stage1.c, stage1.h: Added function Stage1_size()

2007-12-19 03:03  twu

	* src/: resulthr.c, resulthr.h: Added specialized Result_T for
	  GSNAP

2007-12-19 03:02  twu

	* src/reqpost.h: Added conditional include of resulthr.h for GSNAP

2007-12-19 02:55  twu

	* src/: params.c, params.h: Removed obsolete fields

2007-12-19 02:54  twu

	* src/: matchpair.c, matchpair.h: Removed obsolete functions

2007-12-19 02:53  twu

	* src/iit-read.c: Removed warning message about not finding a file

2007-12-19 02:51  twu

	* src/stage3.h: Made maponly mode work with Gregion_T objects.

2007-12-19 02:51  twu

	* src/stage3.c: Fixed bug where genomicuc_ptr was NULL.  Made
	  maponly mode work with Gregion_T objects.

2007-12-19 02:49  twu

	* src/: gregion.c, gregion.h: Added fields to Gregion_T for maponly
	  mode.

2007-12-19 02:45  twu

	* src/gmap.c: Restored old maponlyp code.  Added error message if
	  pthreads fails on operating system.

2007-12-19 02:43  twu

	* src/genuncompress.c: Added flag to print one character per line

2007-12-19 02:42  twu

	* src/: blackboard.c, blackboard.h: Added function to see if
	  blackboard is done

2007-12-19 02:41  twu

	* src/: Makefile.gmaponly.am, Makefile.gsnaptoo.am,
	  Makefile.pmaptoo.am: Added commands for GSNAP

2007-12-07 07:37  twu

	* src/pair.c: Fixed bug with trim_end, now an exclusive coordinate
	  rather than an inclusive one.

2007-12-07 06:41  twu

	* cvs2cl.pl: Added changelog program to CVS

2007-12-07 06:23  twu

	* src/gmap.c: Changed calls to Stage1_compute to match new
	  interface

2007-12-07 06:22  twu

	* src/stage1hr.h: Removing unused parameters

2007-12-07 06:21  twu

	* src/stage1hr.c: Corrected positions of 12-mers for sequences
	  shorter than 36 nt.  Reduced final threshold score to 12.
	  Checking for repetitive sequence.

2007-12-07 06:19  twu

	* src/: stage1.c, stage1.h: Separated stage 1 low-resolution
	  procedure from high-resolution procedure.

2007-12-07 06:02  twu

	* src/: oligo.c, oligo.h: Added procedure for counting number of
	  genomic positions for a given oligomer

2007-12-07 06:01  twu

	* src/gsnap.c: Now calling Stage1hr_compute directly.  Removed some
	  unused code.

2007-12-07 06:00  twu

	* src/gmap.c: Restored maponly mode

2007-12-07 05:59  twu

	* src/: block.c, block.h, indexdb.c, indexdb.h: Added procedure for
	  counting number of genomic positions for a given oligomer

2007-12-06 06:05  twu

	* src/stage1hr.c: Initial attempt to generalized procedure to
	  handle oligomers shorter than 36, using initial testing of 3
	  12-mers.

2007-12-01 08:04  twu

	* src/stage1hr.c: Fixed bugs in computation and printing of middle
	  indels.  Fixed bug when best_querypos (in terms of npositions)
	  was -1.

2007-12-01 02:39  twu

	* src/stage1hr.c: Added strategy of using most specific oligomer to
	  drive search for exact matches.

2007-11-30 21:54  twu

	* src/stage1hr.c: Added keep_score parameter to find_segments.

2007-11-30 21:26  twu

	* src/indexdb.c: Made heapify faster.  Hard-coded left_nts and
	  right_nts to be 1 in read_shifted.

2007-11-30 21:24  twu

	* src/genome.c: In Genome_fill_buffer, checking for negative
	  starting coordinate, and filling with N's if necessary.

2007-11-30 09:58  twu

	* src/stage1hr.c: Limited dynamic programming to just the
	  non-matching oligomer, whenever possible.

2007-11-30 05:07  twu

	* src/stage1hr.c: Added a triplet matching step with binary search
	  to find exact matches.  Fixed a bug in find_segments in handling
	  the last diagonal.

2007-11-29 09:24  twu

	* src/stage1hr.c: Changed output format to show substitutions,
	  insertions, and deletions.  Made speed improvements in heap
	  algorithm.

2007-11-29 01:25  twu

	* src/gsnap.c: Simplified code for handling short reads.  Stopped
	  usage of oligoindex.

2007-11-29 01:24  twu

	* src/stage1hr.c: Implemented version that handles indels.  Some
	  speed improvements in reporting exact matches when found.

2007-11-27 09:32  twu

	* src/stage1hr.c: Removed unused code

2007-11-27 09:23  twu

	* src/: stage1hr.c, stage1hr.h: Working version implemented for
	  36-mers, allowing for substitutions

2007-11-27 09:21  twu

	* src/stage1.h: Taking queryseq as an argument for Stage1_compute
	  (needed for gsnap).

2007-11-27 09:20  twu

	* src/stage1.c: Using new interface to Block_process_oligo

2007-11-27 09:18  twu

	* src/Makefile.am: Makefile.am now generated by bootstrap from
	  other files

2007-11-27 09:15  twu

	* src/stage2.c: Added debugging statements

2007-11-27 09:14  twu

	* src/: sequence.c, sequence.h: Added procedure
	  Sequence_print_oneline

2007-11-27 09:14  twu

	* src/: rbtree.c, rbtree.h, rbtree.t.c: Initial import into CVS

2007-11-27 09:11  twu

	* src/: result.c, result.h: Added procedure Result_blank

2007-11-27 09:10  twu

	* src/: params.c, params.h: Removed truncstep

2007-11-27 09:10  twu

	* src/oligoindex.c: Added correct calculation of badoligos

2007-11-27 09:09  twu

	* src/: oligo.c, oligo.h: Providing diagterm information to lookups
	  from indexdb

2007-11-27 09:08  twu

	* src/: indexdb.c, indexdb.h: Changed high-resolution indexdb to be
	  subclassified by adjacent nucleotides, rather than by phase.

2007-11-27 09:07  twu

	* src/: gregion.c, gregion.h: Initial import into CVS

2007-11-27 09:06  twu

	* src/gsnap.c: Adding separate main program for gsnap.

2007-11-27 09:06  twu

	* src/block.h: Added function Block_skipto.  Giving diagterm
	  information to Oligo_lookup.

2007-11-27 09:05  twu

	* src/block.c: Added function Block_skipto.  Revised coordinates
	  assigned to last_querypos.  Giving diagterm information to
	  Oligo_lookup.

2007-11-27 09:03  twu

	* src/: Makefile.gmaponly.am, Makefile.pmaptoo.am: Added hooks for
	  gsnap

2007-11-27 09:01  twu

	* util/fa_coords.pl.in: Improved handling of cases where chromosome
	  is not parsed

2007-11-27 08:59  twu

	* util/gmap_setup.pl.in: Added -H flag to generate high-resolution
	  gmap dbs.

2007-11-26 04:13  twu

	* src/iit_store.c: Fixed bug in handling GFF files

2007-11-13 20:46  twu

	* src/: indexdb.c, indexdb.h: Implemented precise positioning by
	  organizing composite positions according to phase

2007-11-13 02:12  twu

	* src/: result.c, result.h: Remove stage 1 diagnostic information

2007-11-13 02:12  twu

	* src/: matchpair.c, matchpair.h: Making matchpair generate gregion
	  as output from stage 1

2007-11-13 02:11  twu

	* src/gmap.c: Using new interface to stage 1.  Removed maponly
	  output.

2007-11-13 02:09  twu

	* src/: stage1hr.c, stage1hr.h, Makefile.gmaponly.am,
	  Makefile.pmaptoo.am: Moved high-resolution stage 1 algorithm to a
	  different file

2007-11-13 02:00  twu

	* src/: stage1.c, stage1.h: Eliminated diagnostic fields.  Made
	  interface for low-resolution version compatible with
	  high-resolution version.

2007-11-02 11:16  twu

	* src/: stage3.c, stage3.h: Removed matchpairend and Stage3_direct
	  procedure

2007-11-02 11:07  twu

	* src/: stage1.c, stage1.h: Reverting back to 2007-09-28 version

2007-11-02 11:05  twu

	* src/pmapindex.c: Changed order of arguments in a function call

2007-11-02 11:03  twu

	* src/: params.c, params.h: Added slots for truncstep and
	  chromosomal transitions.

2007-11-02 11:01  twu

	* src/: list.c, list.h: Added functions List_insert and
	  List_reinsert.

2007-11-02 11:00  twu

	* src/: indexdb.c, indexdb.h: Added function Indexdb_shiftedp.	For
	  high-resolution indexdbs, added code to merge batches using
	  either a queue or a heap.

2007-11-02 10:51  twu

	* src/: iit-read.c, iit-read.h: Added function
	  IIT_transitions_subset.

2007-11-02 10:50  twu

	* src/gmapindex.c: Added -e flag to specify high-resolution genomic
	  indices

2007-11-02 10:44  twu

	* src/: chrsubset.c, chrsubset.h: Added function
	  Chrsubset_transitions.  Added assumption to Chrsubset_includep.

2007-11-02 10:42  twu

	* src/: chrnum.c, chrnum.h: Added function Chrnum_print_position

2007-11-02 10:41  twu

	* src/block.h: Added function Block_donep.

2007-11-02 10:40  twu

	* src/block.c: Improved debugging output.  Added function
	  Block_donep.

2007-11-02 10:28  twu

	* src/access.h: Added function to report if file exists.

2007-11-02 10:27  twu

	* src/access.c: Improved error messages.  Added function to report
	  if file exists.

2007-10-16 02:03  twu

	* src/stage1.c: Refined high-resolution algorithm

2007-10-11 08:06  twu

	* src/orderstat.c: Included appropriate header files for memcpy

2007-10-08 05:59  twu

	* src/reader.c: Made reader go all the way to the ends of the
	  sequence

2007-10-08 05:59  twu

	* src/sequence.c: Fixed computation of trimlength

2007-10-08 05:58  twu

	* src/: indexdb.c, indexdb.h: Implemented read and write procedures
	  for new genomic index format (trading off position resolution for
	  adjacent nucleotide contents).

2007-10-06 23:42  twu

	* src/stage1.c: Implemented mapping at ends

2007-10-06 10:36  twu

	* src/stage1.c: Completed initial mapping from middle outward

2007-10-05 23:49  twu

	* src/stage1.c: Added computation of best subpaths

2007-10-03 08:17  twu

	* src/stage1.c: Implemented high-resolution mapping, and
	  arbitrarily long matches for the middle of the sequence outward.

2007-09-30 07:39  twu

	* src/stage1.c: Attempt to use diagonals to find genomic position

2007-09-29 08:47  twu

	* src/: genome.c, genome.h: Added Genome_totallength function

2007-09-29 08:16  twu

	* src/: stage1.c, stage1.h: Added procedure to match doubles of
	  truncated indexdb entries

2007-09-28 08:48  twu

	* util/gmap_setup.pl.in: In -S mode (treating each contig as a
	  chromosome), turning off sorting of chromosomes and contigs.

2007-09-28 08:47  twu

	* src/gmapindex.c: Added -S flag to turn off sorting of chromosomes
	  and contigs

2007-09-28 08:47  twu

	* src/: table.c, table.h, tableint.c, tableint.h: Added ability to
	  return keys sorted by timeindex

2007-09-28 06:15  twu

	* src/: stage1.c, trial.c, trial.h: Changes made to scan query
	  sequence from middle outward

2007-09-28 02:36  twu

	* VERSION: Updated version

2007-09-27 05:23  twu

	* src/gmap.c: Fixed bug for -f 9 and -E output when no paths were
	  found

2007-09-26 04:07  twu

	* VERSION: Updated version

2007-09-26 04:07  twu

	* share/index.html: Revised features for 2007-09-26 version

2007-09-26 04:04  twu

	* util/: gmap_update.pl.in: Made new IIT file permissions the same
	  as the old permissions

2007-09-26 02:41  twu

	* src/iit-read.c: Added error messages to various conditions in
	  IIT_read

2007-09-25 06:20  twu

	* src/sequence.c: Fixed reading of sequences with multiple PC line
	  feeds

2007-09-20 08:33  twu

	* src/stage1.c: Kept code that depended on USE_MATCHPOOL and
	  removed alternate (old) code

2007-09-20 08:32  twu

	* src/: block.c, block.h: Put save variables inside Block_T object

2007-09-19 04:00  twu

	* VERSION: Updated version number

2007-09-19 03:59  twu

	* MAINTAINER: Added reminder to do cvs tag

2007-09-19 03:48  twu

	* src/: iit-read.c, iit-read.h, iit-write.c: Moved compute_flanking
	  procedure from iit-read.c to iit-write.c

2007-09-19 03:29  twu

	* util/Makefile.am, util/gmap_update.pl.in, configure.ac: Added
	  gmap_update program

2007-09-19 03:28  twu

	* src/Makefile.am: Added compile instructions for iit_update

2007-09-19 03:27  twu

	* src/iit-write.c: Made stringlen of type off_t (to handle
	  annotations of length greater than can be handled by int).  Added
	  check to make sure stringlen is non-zero.

2007-09-19 03:27  twu

	* src/iit-read.c: Made stringlen of type off_t (to handle
	  annotations of length greater than can be handled by int)

2007-09-19 03:26  twu

	* share/: archive.html, index.html: Made changes for 2007-09-20
	  release

2007-09-18 06:55  twu

	* src/: Makefile.gmaponly.am, Makefile.pmaptoo.am, iit-read.c,
	  iit-read.h, iit-write.c, iit-write.h, iit_update.c: Implemented
	  iit_update program

2007-09-18 06:55  twu

	* src/iit_store.c: Added -v flag to specify desired version

2007-09-17 06:35  twu

	* src/: oligoindex.c, stage2.c: Changed R output for diagonal
	  graphics

2007-09-12 05:01  twu

	* src/gmap.c: Added a check to make sure we don't push NULL for
	  Stage3_T object.

2007-09-12 04:38  twu

	* src/dynprog.c: Fixed bug in Dynprog_dual_break; need to compute
	  matrix scores only to the minimum of length1 and length2.

2007-09-11 08:06  twu

	* src/dynprog.c: Fixed problem where Dynprog_dual_break was exiting
	  unnecessarily; need to be concerned only about shorter distance.

2007-09-11 08:04  twu

	* src/stage3.c: Added cDNA direction to debugging statements

2007-09-11 06:45  twu

	* src/pair.c: Added provision in PMAP to limit coverage to 100%
	  (could exceed previously because of implicit stop codon added at
	  end of query sequence).

2007-09-11 06:43  twu

	* src/: iit_get.c, stage3.c: Added sign argument for getting
	  flanking entries

2007-09-11 06:43  twu

	* src/: iit-read.c, iit-read.h: Added a sign argument for getting
	  flanking entries

2007-09-11 06:43  twu

	* src/get-genome.c: Added flags for accessing from map files
	  entries of a particular direction or tag

2007-09-11 02:42  twu

	* src/stage1.c: Performing filtering based on clustersize only if
	  too many entries and at least one cluster is large.

2007-09-04 02:27  twu

	* src/stage1.c: Removed filtering based on too many matching pairs

2007-08-30 09:42  twu

	* src/: gbuffer.c, gbuffer.h, gmap.c: Removed unused code and
	  parameters from Gbuffer_T

2007-08-30 09:32  twu

	* src/gmap.c: Allocating memory for genomicseg only as needed

2007-08-28 09:23  twu

	* src/: sequence.c, sequence.h, gmap.c, blackboard.c, blackboard.h:
	  Added ability to read input from multiple sequence files

2007-08-28 09:23  twu

	* src/oligoindex.h: Changed calls to reset oligoindex

2007-08-28 09:23  twu

	* src/oligoindex.c: Fixed hang that resulted when no oligomer
	  positions were found.  Eliminated an extra call to
	  Oligoindex_set_inquery.

2007-08-28 09:22  twu

	* src/stage2.c: Changed call to Oligoindex to reset after tally

2007-08-28 09:21  twu

	* src/stage1.c: Modified debugging output

2007-08-28 09:20  twu

	* src/: mem.c, match.c: Enhanced debugging output

2007-08-28 03:31  twu

	* src/: stage2.c, stage2.h: Returned to previous algorithm for
	  finding shifted canonical dinucleotides, but now allocating
	  memory dynamically.

2007-08-28 03:29  twu

	* src/: gbuffer.c, gbuffer.h: Removed pre-allocated memory for
	  finding shifted dinucleotides

2007-08-28 02:59  twu

	* src/stage2.c: Attempt to conserve memory used in finding shifted
	  canonical dinucleotides.  However, results in speed penalty.

2007-08-25 23:59  twu

	* src/: gbuffer.c, gbuffer.h: Removed unused matchscores variable
	  and unnecessary memory allocation.

2007-08-23 10:27  twu

	* util/gmap_uncompress.pl.in: Added a missing space in the output

2007-08-23 09:14  twu

	* util/gmap_uncompress.pl.in: Added coordinates output (with flag
	  '-f 9')

2007-08-22 03:39  twu

	* src/pair.c: Fixed potential divide-by-zero bug

2007-08-20 04:09  twu

	* util/gmap_setup.pl.in: Added a .SUFFIXES: command at top to
	  prevent unexpected behaviors

2007-08-18 00:04  twu

	* src/stage2.c: Added step to recover when all scores at a querypos
	  are negative, by continuing from grand result.

2007-08-16 06:20  twu

	* src/: pair.c, pair.h, stage2.c, stage2.h, stage3.c: Computing
	  defect rate in middle of stage 3, instead of in stage 2

2007-08-15 08:52  twu

	* src/oligoindex.c: Restored amino acid alphabet to 20 from 18.

2007-08-15 08:32  twu

	* src/oligoindex.c: Fixed typo in variable name

2007-08-15 08:31  twu

	* src/stage2.c: Inactivated limit on number of active hits

2007-08-15 08:31  twu

	* src/: Makefile.gmaponly.am, Makefile.pmaptoo.am: Added
	  orderstat.c and orderstat.h to code

2007-08-15 08:30  twu

	* src/: orderstat.c, orderstat.h: Modified procedures to compute
	  order statistics in place and for both doubles and ints.

2007-08-15 08:29  twu

	* src/oligoindex.c: Computing overabundance based on upper
	  percentile of non-zero counts

2007-08-15 08:27  twu

	* src/doublelist.h: Added Id info to header

2007-08-15 08:27  twu

	* src/gmap.c: Fixed memory leak when user segment is provided

2007-08-15 07:05  twu

	* src/: orderstat.c, orderstat.h: Added orderstat to CVS

2007-08-15 05:30  twu

	* src/: oligoindex.c, oligoindex.h: Trial to eliminate limit on
	  maxoligohits

2007-08-15 03:29  twu

	* src/stage2.c: Improved output for graphical debugging

2007-08-15 03:28  twu

	* src/oligoindex.c: Improved debugging output

2007-08-13 02:54  twu

	* src/stage2.c: Fixed problem with debugging output

2007-08-13 02:53  twu

	* src/stage1.c: Added pruning by path sizes

2007-08-13 02:52  twu

	* src/: matchpair.c, matchpair.h: Added a procedure for finding
	  path size of a given matchpair

2007-07-16 06:59  twu

	* src/: Makefile.gmaponly.am, Makefile.pmaptoo.am: Created two
	  specialized Makefile.am files

2007-07-16 05:30  twu

	* src/Makefile.am: Preparing for iit and genome libraries

2007-07-16 05:28  twu

	* bootstrap, bootstrap.gmaponly, bootstrap.pmaptoo: Created
	  separate bootstrap routines for gmap and gmap-plus-pmap

2007-07-16 05:27  twu

	* VERSION: Updated version number

2007-07-16 05:26  twu

	* src/iit-read.c: Computing alphas and betas for iit_dump

2007-07-16 03:46  twu

	* src/iit-read.c: Computing alphas and betas only when needed for
	  flanking

2007-07-16 03:21  twu

	* src/: gmapindex.c, iit-read.c, iit-read.h, iit-write.c,
	  iit-write.h, iit_get.c, iit_store.c, iitdef.h: Added fields for
	  annotation in IITs

2007-07-16 03:21  twu

	* src/indexdb.c: Added monitoring information

2007-06-25 04:58  twu

	* src/iit_store.c: Added -v flag to print IIT version

2007-06-25 04:57  twu

	* src/iit_get.c: Added -U flag to indicate unsigned results

2007-06-25 04:57  twu

	* src/: get-genome.c, plotgenes.c: Providing sortp parameter to
	  IIT_get

2007-06-25 04:57  twu

	* src/genome.c: Added comment

2007-06-25 04:57  twu

	* src/: genome-write.c, segmentpos.c: For version 2 IITs and later,
	  getting sign directly from IIT, rather than from annotation.

2007-06-25 04:53  twu

	* src/gmapindex.c: No longer writing segment length in contig IITs

2007-06-25 04:51  twu

	* src/iit-write.c: Writing alphas and betas for correct calculation
	  of flanking intervals.

2007-06-25 04:50  twu

	* src/: iit-read.c, iit-read.h: Using alphas and betas for correct
	  calculation of flanking intervals.  Added functions IIT_types,
	  IIT_get_all, and IIT_get_all_typed.

2007-06-25 04:47  twu

	* src/interval.h: Added interface for Interval_sign

2007-06-25 04:46  twu

	* src/iitdef.h: Added space for alphas and betas, needed for
	  correct calculation of flanking intervals

2007-06-22 04:17  twu

	* src/dynprog.h: Defined UNKNOWNJUMP to be used for temporary
	  gapholders during stage 3 calculations.

2007-06-22 04:16  twu

	* src/dynprog.c: Returning NULL on all failures, without gapholders
	  (which are now inserted by calling procedures in stage 3).
	  Allowing 5' and 3' extensions to work to maxlength allowed.

2007-06-21 05:20  twu

	* src/iitdef.h: Added version to IIT_T

2007-06-21 05:20  twu

	* src/interval.c: Storing sign for each interval

2007-06-21 05:19  twu

	* src/: iit-read.c, iit-read.h, iit-write.c, iit-write.h:
	  Introduced version 2 format, which stores sign for each interval.
	  Not using annotation anymore to represent sign.  Added function
	  IIT_find_multiple.

2007-06-20 13:19  twu

	* src/pairpool.c: Improved debugging statements

2007-06-20 13:19  twu

	* src/: gdiag.c, get-genome.c, gmap.c, iit-read.c, iit-read.h,
	  iit_get.c, interval.c, interval.h, plotgenes.c, segmentpos.c,
	  stage3.c: Added ability to sort intervals by coordinates in
	  IIT_get routines

2007-06-20 12:05  twu

	* src/mem.c: In comments, showing how TRAP should be defined

2007-06-20 12:04  twu

	* src/stage3.c: Whenever dynprog procedure returns NULL, make sure
	  to put back peeled pairs and insert a gapholder.  Fixes a bug in
	  BQ672778 against hg18.  Jumps in gapholders now calculated only
	  in certain procedures.

2007-06-06 12:53  twu

	* src/stage3.c: Removed abort commands on peels that run into gaps

2007-06-06 12:52  twu

	* src/dynprog.c: Expanded on comment

2007-06-04 02:36  twu

	* VERSION, share/index.html: Updated version

2007-06-04 02:31  twu

	* src/dynprog.c: Removed insertion of gapholder for a single gap
	  that is too long to solve.

2007-06-02 06:39  twu

	* src/stage1.c: Added debugging statement to signal end of stage 1

2007-06-02 06:39  twu

	* src/dynprog.c: Eliminated allocation of temporary Dynprog_T
	  objects

2007-06-02 06:38  twu

	* src/pair.c: Now printing query_skip in -A and -S output

2007-05-29 06:44  twu

	* src/dynprog.c: Lowered gap penalties for single gaps.  Fixed bug
	  in solving dynamic programming for lower-case input sequences.

2007-05-29 06:11  twu

	* src/stage3.c: Added procedures for cleaning non-matches at ends
	  of alignment, which are always called.

2007-05-29 04:12  twu

	* src/stage3.c: Removing all nonmatches at 5' and 3' ends

2007-05-25 02:13  twu

	* VERSION: Updated version

2007-05-25 02:13  twu

	* share/index.html: Made changes to reflect 2007-05-25 version

2007-05-25 02:12  twu

	* src/: pair.c, pair.h, stage3.c: Added coverage and identity
	  information to GFF3 output

2007-05-25 01:40  twu

	* share/: archive.html, index.html: Made changes to reflect
	  2007-05-25 version

2007-05-24 01:57  twu

	* configure.ac: Checking both fixed and variable mapping for mmap

2007-05-24 01:55  twu

	* util/fa_coords.pl.in: Fixed problem in parsing lines containing
	  the word "chromosome"

2007-05-24 01:55  twu

	* src/stage3.c: Fixed bug in solving dual breaks

2007-05-24 01:53  twu

	* src/pair.c: Fixed PSL output so query and target gaps are
	  computed directly from the block starts and lengths.

2007-05-24 01:52  twu

	* src/gmap.c: Added flag -j for showing dual breaks

2007-05-24 01:51  twu

	* src/dynprog.c: Fixed bug where solution of dual break exceeded
	  minimum gap

2007-05-15 07:17  twu

	* src/stage3.h: Added do_final_p parameter to Stage3_compute

2007-05-15 07:16  twu

	* src/stage3.c: Incorporating procedure to trim bad middle exons

2007-05-15 07:13  twu

	* src/stage1.c: Performing salvage if total number of matches is
	  relatively low

2007-05-15 07:12  twu

	* src/smooth.c: Added to exon length in smoothing for short exons

2007-05-15 07:12  twu

	* src/pair.c: Added test code to print information about extra
	  exons

2007-05-15 07:11  twu

	* src/intron.c: Removing call to abort.

2007-05-15 07:11  twu

	* src/dynprog.c: Added code to bridge dual break with rewards for
	  canonical introns.  Tweaked some parameters, including less
	  penalty for gap extensions.

2007-04-25 10:58  twu

	* src/mem.c: Added error messages for memory allocation problems

2007-04-25 10:58  twu

	* src/gmap.c: Added -X flag for heavily favoring canonical and
	  semi-canonical introns

2007-04-23 05:20  twu

	* src/gmap.c: Made strict translation the default again

2007-04-23 04:35  twu

	* src/indexdb.c: Added "U" to integers in bit operations

2007-04-23 04:34  twu

	* src/genome.c: Using two arrays instead of one for translate.

2007-04-23 04:34  twu

	* src/compress.c: Using two arrays instead of one for translate.
	  Added various abort checks.

2007-04-23 04:07  twu

	* src/translation.c: Removed unnecessary checks of extraexonp

2007-04-23 04:07  twu

	* src/pair.c: Fixed Pair_dump_one so it handles extraexonp flag

2007-04-23 03:50  twu

	* src/pairpool.c: Fixed bug in assigning extraexonp

2007-04-23 03:50  twu

	* src/pair.c: Changed add_intronlengths slightly

2007-04-23 03:33  twu

	* config/acx_mmap_variable.m4: Moved AC_DEFINE out of macro, to be
	  called explicitly in configure.ac

2007-04-23 03:32  twu

	* config/acx_mmap_fixed.m4: Added macro for testing mmap with
	  MAP_FIXED

2007-04-23 03:02  twu

	* src/gmap.c: Made frameshift-tolerant translation the default

2007-04-23 03:01  twu

	* src/pair.c: Changed output of CDS in gff3 mode to produce an
	  in-frame protein sequence

2007-04-23 02:10  twu

	* src/translation.h: Added strictp for PMAP.

2007-04-23 02:10  twu

	* src/translation.c: Added strictp for PMAP.  Handling extraexonp
	  items in alignment.

2007-04-23 02:09  twu

	* src/stage3.c: Giving extraexonp information to pairpool
	  procedures for gapalign items

2007-04-23 02:08  twu

	* src/pair.h: Added procedure for computing fractional error.

2007-04-23 02:08  twu

	* src/pair.c: Added provisions for handling extraexonp flag.  Added
	  procedure for computing fractional error.

2007-04-23 02:07  twu

	* src/: pairpool.c, pairpool.h: Added provisions for handling
	  extraexonp flag

2007-04-23 02:07  twu

	* src/pairdef.h: Added flag for extra cDNA exon

2007-04-23 02:06  twu

	* src/comp.h: Added comp for extra cDNA exon

2007-04-23 01:55  twu

	* src/stage3.h: Added strictp for PMAP.

2007-04-23 01:54  twu

	* src/stage3.c: Added procedures for trimming internal exons with
	  poor matches, and for finding extra exons in a dual break.  Added
	  strictp for PMAP.

2007-04-23 01:52  twu

	* src/: dynprog.c, dynprog.h: Added procedures for finding extra
	  exons in a dual break

2007-04-23 01:48  twu

	* src/compress.c: Provided more informative error message

2007-04-23 01:33  twu

	* src/oligoindex.c: Handled an arithmetic error caused by divide by
	  zero

2007-04-23 01:26  twu

	* src/gmap.c: Added flag -H for handling trimming middle exons and
	  reporting of dual breaks.  Removed flag -j.  Allowed strictp to
	  be used in PMAP.

2007-04-16 10:23  twu

	* tests/: align.test.ok, map.test.ok: Made test output match
	  current output

2007-04-16 10:22  twu

	* config/acx_mmap_variable.m4, configure.ac: Added check for mmap
	  using MAP_VARIABLE (because AIX fails on MAP_FIXED)

2007-04-16 10:17  twu

	* src/gmap.c: Fixed global variables not used in PMAP

2007-04-16 10:16  twu

	* src/stage2.c: Fixed check for negative scores to work for PMAP

2007-04-16 09:46  twu

	* src/stage1.c: Placing bound on number of samples taken over query
	  sequence

2007-04-16 09:46  twu

	* src/stage2.c: For very long sequences, pruning based on clear
	  coverage

2007-04-16 09:46  twu

	* src/: oligoindex.c, oligoindex.h: Added computation of clear
	  coverage (percent of query sequence covered by relatively few
	  diagonals).

2007-04-16 09:45  twu

	* src/matchpair.c: Added debugging statements

2007-04-06 07:34  twu

	* src/stage2.c: Added restriction on distance for grand lookback.
	  Added check on nactive for scoring at querypos.

2007-04-06 03:14  twu

	* src/stage2.c: Added nactive as a filter in stage 2

2007-04-02 08:05  twu

	* src/stage2.c: Added comment about a way to restrict debugging
	  output

2007-04-02 08:04  twu

	* src/iit-read.c: Added start/end information to endpoints in
	  dumping counts

2007-03-08 07:44  twu

	* src/stage2.c: Quitting if totalpositions is zero

2007-03-08 07:43  twu

	* src/gmap.c: Enabled table output (-f 9) for relative alignment
	  mode (-w).

2007-03-03 04:59  twu

	* src/stage2.c: Fixed bug which led to the partial fill problem in
	  filling oligomers

2007-03-02 07:57  twu

	* src/Makefile.am: Added pthread_libs for iit utilities

2007-03-01 07:56  twu

	* src/gdiag.c: Added printing of centromere regions.  Printing
	  marginals more efficiently.

2007-03-01 07:54  twu

	* src/Makefile.am: Added chrnum and chrsubset files to gdiag

2007-03-01 07:54  twu

	* src/: iit-read.c, iit-read.h: Made IIT_transitions function
	  return signs

2007-02-28 00:37  twu

	* src/gdiag.c: Added flag for ignoring main diagonal.  Fixed
	  problem with printing revcomp diagonals.  Added code for
	  computing different types of patterns.

2007-02-21 03:17  twu

	* src/gdiag.c: Added hooks for user to enter chromosomal subsets

2007-02-21 03:16  twu

	* src/complement.h: Added a character code string that doesn't
	  convert to uppercase, for gdiag.

2007-02-20 07:27  twu

	* src/gdiag.c: Added ability to use map iit files.  Skipping over
	  masked regions in determining lookback.

2007-02-20 04:42  twu

	* src/gdiag.c: Fixed bug in retrieving last part of sequence from
	  gmapdb.  Providing flag to ignore lowercase (e.g., masked)
	  characters in query.

2007-02-20 02:13  twu

	* src/gdiag.c: Added ability for user to provide genomic segment

2007-02-20 01:03  twu

	* src/Makefile.am: Added iit-write source files for gdiag

2007-02-20 01:03  twu

	* src/gdiag.c: Fixed bug where genomestart could be less than
	  genomeend in a diagonal.  Made separate procedures for updating
	  forward and revcomp diagonals.

2007-02-20 01:01  twu

	* src/: indexdb.c, indexdb.h: Added procedure IIT_read_inplace for
	  gdiag.

2007-02-20 01:01  twu

	* src/iit-write.h: Added procedure IIT_new to allow creation and
	  use of iit in the same program.

2007-02-20 01:01  twu

	* src/iit-write.c: Added procedure IIT_new to allow creation and
	  use of iit in the same program.  Simplified code for Node_fwrite.

2007-02-20 00:59  twu

	* src/: iit-read.c, iit-read.h: Added procedure IIT_transitions

2007-02-18 11:45  twu

	* src/gdiag.c: Added a ring structure to increase speed

2007-02-18 04:53  twu

	* src/genome.h: Added procedures for gdiag

2007-02-18 04:50  twu

	* src/gdiag.c: Made speed improvements by not storing full 24-mers,
	  but rather storing results of previous 12-mers

2007-02-18 04:49  twu

	* src/genome.c: Added procedures for gdiag

2007-02-18 03:45  twu

	* src/gdiag.c: Added calculation of diagonals, ability to read
	  query from gmapdb, and storage of intervals.

2007-02-16 09:45  twu

	* src/: Makefile.am, gdiag.c: Added program gdiag

2007-02-12 01:36  twu

	* src/gmap.c: Increased parameter for maxoligohits

2007-02-12 01:36  twu

	* src/stage3.c: Lowered parameter for intronlen

2007-02-12 01:36  twu

	* src/stage2.h: Removed unused function

2007-02-12 01:36  twu

	* src/stage2.c: Changed distance penalty to consider both
	  gendistance (now linearly, instead of logarithmically) and
	  querydistance (quadratically).  Using both maxnconsecutive and
	  pct_coverage to decide whether to continue with stage 2.

2007-02-12 01:31  twu

	* src/stage1.c: Reduced parameter for number of trials

2007-02-12 01:31  twu

	* src/pair.c: Fixed calculation of coverage for PMAP

2007-02-12 01:29  twu

	* src/oligoindex.h: Moved parameters here

2007-02-12 01:29  twu

	* src/oligoindex.c: Implemented algorithm for PMAP.  Allowing a
	  diagonal to dominate only if it is completely consecutive.

2007-02-09 03:49  twu

	* src/: iit-read.c, iit-read.h: Added function to dump labels

2007-02-09 02:12  twu

	* src/gmap.c: Fixed bugs with map iit files: bad test for
	  distinguishing between universal map files and chromosomal map
	  files, and incorrectly checking map tags against chromosomal iit.

2007-02-08 10:06  twu

	* src/: oligoindex.c, oligoindex.h: Added computation of percent
	  coverage by diagonals

2007-02-08 05:30  twu

	* src/access.c: Added a debugging statement

2007-02-08 02:04  twu

	* src/gmap.c: Fixed floating point error when trimoligos is zero

2007-02-08 01:59  twu

	* src/: gmap.c, oligoindex.c, oligoindex.h, stage2.c, stage2.h:
	  Added graphical debugging output for stage 2

2007-02-07 10:05  twu

	* src/smooth.c: Distinguishing use of genomejump and queryjump
	  lengths in pre-single-gap smoothing versus post-single-gap
	  smoothing.

2007-02-07 07:14  twu

	* src/gmap.c: Fixed floating exception when sequence has no oligos

2007-02-07 04:21  twu

	* src/stage2.c: Initializing guide in 5' trim region, until first
	  hits are found.

2007-02-07 02:26  twu

	* src/gmap.c: Changed default pruning behavior to be no pruning.

2007-02-07 02:25  twu

	* src/oligoindex.c: Made speed improvements in scanning diagonals.
	  Removed old code for computing maxconsecutive.

2007-02-06 16:38  twu

	* src/: oligoindex.h, stage2.c: Changed name of variable

2007-02-06 16:38  twu

	* src/oligoindex.c: Eliminated convex hull algorithm and
	  implemented method based on ordering of diagonals.

2007-02-06 16:35  twu

	* src/: diag.c, diag.h: Removed unused procedures

2007-02-06 10:44  twu

	* src/oligoindex.c: Implemented a convex hull algorithm to
	  determine minactive and maxactive bounds.

2007-02-06 10:43  twu

	* src/: diag.c, diag.h: Added a procedure to sort diagonals based
	  on closeness to origin

2007-02-06 06:53  twu

	* src/: oligoindex.c, oligoindex.h, stage2.c: Restored computation
	  of maxgoodconsecutive to filter out bad stage1 candidates

2007-02-06 04:24  twu

	* src/stage2.c: Allowing fill of nucleotides to occur even when
	  querypos/lastquerypos or genomepos/lastgenomepos are too close.

2007-02-06 04:23  twu

	* src/oligoindex.c: Added new procedure for determining dominance
	  among diagonals

2007-02-06 04:22  twu

	* src/: diag.c, diag.h: Added procedure for sorting by nconsecutive

2007-02-05 22:33  twu

	* src/stage2.c: Using minactive and maxactive to bound current
	  querypos, and active to determine available hits for previous
	  querypos.

2007-02-05 22:32  twu

	* src/: oligoindex.c, oligoindex.h: Computing diagonals inside
	  Oligoindex_get_mappings procedure.  Implemented simple dominance
	  procedure.

2007-02-05 22:30  twu

	* src/: diag.c, diag.h, diagdef.h, diagpool.c, diagpool.h: Added
	  fields for nconsecutive and dominancep

2007-02-05 08:00  twu

	* src/oligoindex.c: Changes in parameters

2007-02-05 08:00  twu

	* src/stage2.c: Changes to debugging output

2007-02-05 05:28  twu

	* src/oligoindex.c: Speed improvements by inlining calls to Intlist
	  accessors

2007-02-05 04:39  twu

	* src/stage2.h: Removed unused function

2007-02-05 04:39  twu

	* src/: oligoindex.h, stage2.c: Using length as a criterion instead
	  of nconsecutive for proceeding to dynamic programming

2007-02-05 04:38  twu

	* src/oligoindex.c: Reduced requirement for nconsecutive in
	  scanning diagonals.  Keeping cumulative track of highest and
	  lowest diagonals.  Added extra_bounds to diagonal bounds.

2007-02-05 03:34  twu

	* src/: Makefile.am, diag.c, diag.h, diagdef.h, diagpool.c,
	  diagpool.h, gmap.c: Adding Diag_T and Diagpool_T objects for
	  scanning diagonals

2007-02-05 03:33  twu

	* src/: oligoindex.c, oligoindex.h, stage2.c, stage2.h: Scanning
	  diagonals to set bounds on active oligomers

2007-02-04 15:45  twu

	* src/: Makefile.am, gmap.c, intpool.c, intpool.h, oligoindex.c,
	  oligoindex.h, stage2.c, stage2.h: Added Intpool_T object to
	  manage storage for Intlist_T objects

2007-02-04 15:15  twu

	* src/gmap.c: Using new interface to Stage3_compute

2007-02-04 15:14  twu

	* src/stage2.c: In dynamic programming, added a lookback to the
	  grand best querypos and hit

2007-02-04 15:13  twu

	* src/: intlist.c, intlistdef.h: Provided exposure to internal
	  structure of Intlist_T

2007-02-03 13:19  twu

	* src/: oligoindex.c, oligoindex.h, stage2.c: Implemented faster
	  algorithm for identifying active stage 2 oligomers.

2007-02-03 08:50  twu

	* src/stage2.h: Removed unused procedures

2007-02-03 08:49  twu

	* src/: oligoindex.c, oligoindex.h, stage2.c: Implemented
	  procedures to skip over unused mappings, based on active

2007-02-02 03:15  twu

	* src/: gmap.c, oligoindex.c, oligoindex.h, stage2.c, stage2.h:
	  Implemented new stage 2 procedure.  Now using oligoindex at
	  minindexsize and filtering those hits according to a local
	  search.  Initial search is based on maxindexsize.  Uncovered ends
	  of the alignment receive a looser local search criterion.
	  Increased stage 2 lookback from 60 to 100.

2007-02-02 03:09  twu

	* src/translation.c: Fixed bug where first cDNA amino acid appeared
	  under a cDNA space.

2007-02-02 03:08  twu

	* src/stage1.c: Adding one more trial for long sequences

2007-02-02 03:07  twu

	* src/pair.c: Computing coverage and now trimmed coverage at print
	  time.  Added output line for trimmed coverage.  Added trim
	  information in compressed (-Z) output.  Adjusting output of trim
	  boundaries based on alignment.

2007-02-02 03:05  twu

	* src/: stage3.h, pair.h: Computing coverage and now trimmed
	  coverage at print time.

2007-02-02 03:04  twu

	* src/stage3.c: Computing coverage and now trimmed coverage at
	  print time.  Increased parameter for minintronlength.

2007-02-02 02:14  twu

	* src/gmap.c: Removed -X (cross-species) flag

2007-01-31 08:37  twu

	* src/oligoindex.c: Added code for 18-amino-acid alphabet

2007-01-31 08:36  twu

	* src/gmap.c: Made user_stage1p false

2007-01-31 08:17  twu

	* src/stage2.c: Trying to make penalties consistent across
	  different cases

2007-01-31 01:26  twu

	* src/stage3.c: Initialized variables in Stage3_T object

2007-01-31 01:26  twu

	* src/pair.c: Fixed memory leak in gff exon mode (-f 2)

2007-01-07 02:34  twu

	* src/stage3.c: If both single and dual gap solutions are
	  canonical, picking solution with best score.

2007-01-06 05:54  twu

	* src/dynprog.c: Made reward for final canonical intron uniform
	  across defect rates.	Boosted reward for final semicanonical
	  intron to match that for canonical intron.

2007-01-04 22:23  twu

	* src/pair.c: Fixed dinucleotide output in compressed (-Z) format
	  when user-provided genomic segment has lower-case characters.

2007-01-04 04:25  twu

	* src/stage2.c: Reduced value of EQUAL_DISTANCE, to favor better
	  local alignment over longer global alignment

2007-01-04 04:20  twu

	* src/stage3.c: Counting exons only after gaps filled in

2007-01-04 04:19  twu

	* src/: pair.c, pair.h: Added procedure for counting exons after
	  gaps filled in

2007-01-03 06:04  twu

	* src/dynprog.c: Made one-sided gap behavior true only for single
	  gaps and end gaps

2007-01-03 05:03  twu

	* src/stage3.c: Removed fix_pmap_holes function and all references
	  to it

2006-12-17 23:38  twu

	* share/index.html: Updated version

2006-12-17 21:20  twu

	* VERSION: Updated version

2006-12-17 21:20  twu

	* src/translation.c: Prevented assignment of incomplete last codon
	  on cDNA side in strict mode

2006-12-17 21:19  twu

	* src/stage1.c: Removed unused variables

2006-12-17 21:19  twu

	* src/matchpair.c: Increased EXTRA_SHORTEND

2006-12-17 21:19  twu

	* src/gmap.c: Reduced default trimexonpct.  Changed bandwidths for
	  single and gap gaps.

2006-12-17 21:18  twu

	* src/dynprog.c: Added onesidegap behavior, which allows gaps on
	  either genomic or cDNA side, but not both.  Added concept of
	  fixeddestp, which is not true for the ends.

2006-12-14 22:05  twu

	* VERSION: Updated version

2006-12-14 22:05  twu

	* share/index.html: Made changes to reflect new version and strict
	  translation as default

2006-12-14 21:42  twu

	* src/gmap.c: Reduced extraband_end

2006-12-14 21:22  twu

	* src/: dynprog.c, gmap.c: Reduced extraband_single to prevent gaps
	  from being inserted on both sides

2006-12-14 20:00  twu

	* src/: gmap.c, pair.c, pair.h, sequence.c, sequence.h, stage3.c:
	  For PMAP, adding an implicit stop codon at end of sequence if not
	  already present, and distinguishing between computational
	  fulllength and given fulllength.

2006-12-14 19:59  twu

	* src/smooth.c: Changed probability threshold for identifying short
	  exons

2006-12-14 06:03  twu

	* src/gmap.c: Made strict translation the default, and tolerant
	  translation turned on by -Y flag

2006-12-14 05:57  twu

	* src/stage3.c: Providing pound signs in dual breaks in diagnostic
	  output.  Replacing backtranslation characters with 'N' in PMAP
	  output.  Removed microexon search from PMAP.	Using single gap
	  procedure instead of fix_pmap_holes procedure for PMAP.

2006-12-14 05:47  twu

	* src/pair.c: Counting ambiguous characters as matches in all
	  instances of computing percent identity

2006-12-14 05:47  twu

	* src/indexdb.h: Added variables for 5-aa mers

2006-12-14 05:46  twu

	* src/dynprog.c: Limiting bandwidth in single gap alignment to be
	  dependent on differences in segment lengths

2006-12-14 05:46  twu

	* src/backtranslation.c: Not performing backtranslation if any
	  genomic codon position is blank.

2006-12-14 05:44  twu

	* src/md5.t.c: Removed unused file

2006-12-13 04:52  twu

	* src/dynprog.c: Reduced width of band in single gaps when lengths
	  are equal

2006-12-13 04:37  twu

	* src/translation.c: Fixed strict translation mode, so it begins as
	  same location as genomic translation.

2006-12-13 04:37  twu

	* src/stage3.c: Removed step of merging adjacent dynamic
	  programming.	Using two different smoothing steps.  Protected
	  small introns from being solved as single gaps in final intron
	  pass.

2006-12-13 04:34  twu

	* src/: smooth.c, smooth.h: Created two separate smoothing
	  procedures, one based on net gap, and one based on size.

2006-12-13 04:33  twu

	* src/dynprog.c: For cDNA gaps, inserting indel pairs only if both
	  gaps are small

2006-12-12 02:14  twu

	* tests/map.test.ok: Added blank line at end

2006-12-12 02:14  twu

	* VERSION: Updated version

2006-12-12 02:14  twu

	* MAINTAINER: Added reminder to check cvs log to make sure files
	  are all up to date

2006-12-12 02:12  twu

	* src/stage3.c: Removing gaps at 5' and 3' ends after end
	  extensions.  Checking for division by zero in trim_bad_exons.

2006-12-12 02:12  twu

	* src/Makefile.am: Simplified list of source files

2006-12-08 08:00  twu

	* share/archive.html: Updated to reflect 2006-12-08 version

2006-12-08 07:57  twu

	* share/archive.html: Merged into trunk

2006-12-08 07:43  twu

	* tests/defs: Initial import into CVS

2006-12-08 07:40  twu

	* tests/: map.test.ok, setup1.test.in, setup2.test.in: Merged into
	  trunk

2006-12-08 07:36  twu

	* tests/: coords1.test.in, coords1.test.ok, iit_dump.test.in,
	  iit_get.test.in, iit_store.test.in, map.test.in: Merged into
	  trunk

2006-12-08 07:33  twu

	* tests/: Makefile.am, align.test.in, align.test.ok: Merged into
	  trunk

2006-12-08 01:40  twu

	* config.site.gne, share/index.html, util/pmap_setup.pl.in: Merging
	  into trunk

2006-12-08 01:36  twu

	* VERSION: Merging into trunk

2006-12-08 01:33  twu

	* MAINTAINER: Merging into main trunk

2006-12-08 00:57  twu

	* tests/iit.test.in: Combined iit_store, iit_get and iit_dump tests
	  into one script

2006-12-08 00:35  twu

	* src/stage1.c: Increased definition of short sequence (for
	  allowing cluster mode) for PMAP

2006-12-08 00:34  twu

	* src/match.c: Fixed printing of sequences in debugging statements

2006-12-08 00:33  twu

	* VERSION: Updated version

2006-12-08 00:32  twu

	* share/index.html: Revised to report 2006-12-08 version

2006-12-05 03:42  twu

	* src/stage3.c: Fixed miscount problem with filling in short
	  introns.  Increased MININTRONLEN_FINAL significantly.

2006-12-01 07:21  twu

	* src/stage1.c: Printing chromosome name in debugging statements

2006-12-01 07:20  twu

	* src/: match.c, match.h: Added procedure Match_chr

2006-11-30 07:56  twu

	* src/stage3.c: Allowing and correcting for gaps after gaps

2006-11-30 07:39  twu

	* src/smooth.c: Using difference between genomejump and queryjump
	  to define introns for the purposes of smoothing.

2006-11-30 01:25  twu

	* configure.ac: Added check for sigaction

2006-11-30 01:25  twu

	* README: Updated README file

2006-11-30 01:24  twu

	* MAINTAINER: Removed reminder to check for CHECK

2006-11-30 01:24  twu

	* util/md_coords.pl.in: Fixed behavior when user wants only the
	  reference strain

2006-11-30 01:23  twu

	* util/gmap_setup.pl.in: Changed name from raw to fullascii.
	  Changed default for PMAP from 7 to 6.

2006-11-30 01:22  twu

	* util/gmap_process.pl.in: Added check to see that all contigs are
	  processed

2006-11-30 01:18  twu

	* src/stage3.c: Assigning gap pairs after final extensions of 5'
	  and 3' ends

2006-11-30 01:17  twu

	* src/smooth.c: Removed include of unused header file

2006-11-30 01:16  twu

	* src/gmap.c: Stopped warning message for -B when flag was not
	  provided

2006-11-30 01:15  twu

	* src/: genome-write.c, gmapindex.c, indexdb.c, indexdb.h,
	  pmapindex.c: Added genome name to monitoring statements

2006-11-28 04:45  twu

	* src/stage1.c: Revised heuristics for determining maxtotallen and
	  lengths for extensions

2006-11-28 04:44  twu

	* src/gmap.c: Ignoring batch flag if only a single sequence is
	  given

2006-11-27 09:35  twu

	* src/stage1.c: Removed unused code

2006-11-27 09:35  twu

	* src/matchpair.c: Adding extra extension length when continuousp
	  is false

2006-11-27 08:54  twu

	* src/gmap.c: Revised default lengths for single intron length and
	  total genomic length

2006-11-27 08:53  twu

	* src/dynprog.c: Added checks for genomic segment at ends being
	  shorter than query segment

2006-11-27 08:53  twu

	* src/indexdb.h: Using 6-mers with full alphabet in PMAP

2006-11-27 08:52  twu

	* src/indexdb.c: Improved monitoring statements

2006-11-27 08:51  twu

	* src/: matchpair.c, matchpair.h: Revised procedures for computing
	  support and extensions.  Integrated procedures for filtering of
	  unique and duplicate matchpairs.

2006-11-27 08:50  twu

	* src/oligoindex.c: Returned to 20 amino acids in stage 2

2006-11-27 08:50  twu

	* src/: stage1.h, params.c, params.h: Removed unused variable

2006-11-27 08:49  twu

	* src/stage1.c: Integrated matchpairs into a single list.  Revised
	  procedures for extending genomic region based on 12-mers.

2006-11-27 08:48  twu

	* src/stage3.c: Allowed arbitrarily long incursion into previous
	  dynprog during peelback.

2006-11-27 08:47  twu

	* src/stage2.c: Separated fwd_consecutive and rev_consecutive.
	  Made values consistent regardless of indexsize.

2006-11-21 09:55  twu

	* src/stage1.c: Fixed extensions for PMAP

2006-11-21 07:40  twu

	* src/indexdb.c: Reversed previous changes to try to make
	  idxpositions file point to end of oligomer for reverse strand
	  matches.

2006-11-21 07:33  twu

	* src/indexdb.c: Made idxpositions file point to end of oligomer
	  for reverse strand matches.  Improved debugging output.

2006-11-21 07:32  twu

	* src/stage1.c: Added a binary search routine

2006-11-20 09:26  twu

	* src/: stage1.c, indexdb.h: Made changes for PMAP to work with
	  6-mer pmapdb

2006-11-20 06:18  twu

	* src/oligoindex.c: Fixed debugging statements for PMAP

2006-11-20 06:16  twu

	* src/pair.c: Revised psl protein output for matches to the
	  negative genome strand

2006-11-20 04:42  twu

	* src/: backtranslation.c, backtranslation.h: Made an extern
	  procedure for computing consistent codon for a given amino acid.

2006-11-20 04:42  twu

	* src/: translation.c, translation.h: Made get_codon an extern
	  procedure

2006-11-20 04:41  twu

	* src/stage3.c: Added procedure for fixing alignment holes in PMAP.
	  Applying higher standard for accepting dual intron solutions.

2006-11-20 04:40  twu

	* src/stage2.c: Fixing bugs in identifying stage 2 candidates to
	  abort

2006-11-20 04:38  twu

	* src/gmap.c: Setting trim variables appropriately in maponly mode

2006-11-20 04:38  twu

	* src/dynprog.c: In PMAP, rounding up or down to finish codon

2006-11-16 10:42  twu

	* src/stage3.c: Using intron types to evaluate bad exons at ends.
	  Adding another round of extensions at ends after trimming of bad
	  exons.  Restored correction for genomepos at left end skip when
	  filling in introns.

2006-11-16 10:40  twu

	* src/dynprog.c: Assigning intron type for microexons added at ends
	  of alignment

2006-11-16 10:40  twu

	* src/: gbuffer.c, gbuffer.h: Removed unused variables

2006-11-16 10:40  twu

	* src/stage2.c: Removed unused variables.  Using correct value for
	  maxconsecutive instead of last one.

2006-11-15 11:06  twu

	* src/stage3.c: Using uppercase string, with U-to-T conversion, to
	  identify mismatches in peelback procedures.

2006-11-15 11:05  twu

	* src/: translation.c, backtranslation.c: Using uppercase string,
	  with U-to-T conversion, instead of toupper().

2006-11-15 11:04  twu

	* src/sequence.c: Using new complement and uppercase strings

2006-11-15 11:04  twu

	* src/pair.c: Using new name for (lowercase) complement string.
	  Including 'U' and 'u' as known bases for computing percent
	  identity.

2006-11-15 11:03  twu

	* src/indexdb.c: Using uppercase string, which also performs U-to-T
	  conversion, instead of toupper().

2006-11-15 11:02  twu

	* src/: genome-write.c, genome.c: Using new name for (lowercase)
	  complement string.

2006-11-15 11:02  twu

	* src/compress.c: Using uppercase string instead of toupper.
	  Compress_get_char() no longer converts characters to uppercase.

2006-11-15 11:00  twu

	* src/dynprog.c: Made U and T a matching pair.	Commented out old
	  code dealing with lowercase characters.

2006-11-15 11:00  twu

	* src/complement.h: Added strings for uppercase of complement, and
	  for U-to-T conversion during uppercase

2006-11-15 09:38  twu

	* src/sequence.c: Enabled removal of spaces in read procedure

2006-11-13 17:53  twu

	* src/dynprog.c: Reduced extension penalties for single gaps

2006-11-13 17:52  twu

	* src/stage3.c: Fixed bug in filling in gaps where leftpair has a
	  genome gap.  Increased size of MININTRONLEN to avoid finding
	  introns in single gap regions.

2006-11-12 12:09  twu

	* src/stage3.h: Added parameter for number of flanking sequences to
	  Stage3_print_map

2006-11-12 12:09  twu

	* src/stage3.c: In 5' and 3' extensions, evaluating continuations
	  before and after a gap if one is found during peeling, and
	  performing microexon search medial to the gap

2006-11-12 12:07  twu

	* src/dynprog.c: Returning null in genome gap if queryjump <= 1

2006-11-12 12:05  twu

	* src/get-genome.c: Added -u flag for printing flanking intervals

2006-11-12 12:05  twu

	* src/: iit-read.c, iit-read.h: Added option to print iit entries
	  in reverse order

2006-11-12 12:04  twu

	* src/indexdb.h: Restored previous parameters

2006-11-12 12:04  twu

	* src/pair.c: Added pointer to pair in debugging output

2006-11-11 09:26  twu

	* src/stage3.c: Fixed computation of bad end exons.  Included short
	  end exons in definition of bad end exons.  Finding bad end exons
	  after 5' and 3' extensions.  Fixed declaration of sense/antisense
	  when no canonical or semicanonical introns are present.  Removing
	  end introns during peelback before 5' and 3' extensions.  Removed
	  unused code for trimming alignment at ends.

2006-11-06 07:19  twu

	* src/gmap.c: Added flags for printing flanking IIT hits and for
	  trimming end exons

2006-11-06 07:18  twu

	* src/stage3.c: Fixed bug in trimming empty alignment

2006-11-06 07:17  twu

	* src/smooth.c: Fixed bug in handling lower-case query sequences

2006-11-01 10:21  twu

	* src/translation.c: Fixed bug in strict translation

2006-11-01 10:20  twu

	* src/iit-read.h: Added procedures for finding flanking hits.

2006-11-01 10:19  twu

	* src/iit-read.c: Made IIT_get more efficient.	Added procedures
	  for finding flanking hits.

2006-11-01 10:19  twu

	* src/iit_get.c: Added -u flag for printing flanking hits

2006-11-01 06:31  twu

	* src/: stage3.c, stage3.h: Allowing trimming of bad exons at ends.
	  Increased peelback at ends.	Added iterative cycles of intron
	  finding within smoothing and dual intron cycles.

2006-11-01 06:30  twu

	* src/smooth.c: Relaxing requirements for short exons at ends,
	  because of later trimming of poor exons at ends

2006-11-01 06:30  twu

	* src/pair.c: Adding printing of intron type for debugging

2006-11-01 06:29  twu

	* src/gmap.c: Stopping deletion of global_except_key, because
	  worker threads may still need it.  Increasing standards for
	  defining a sequence to be repetitive.  Eliminating -U flag for
	  trimming alignments, and adding -k flag for specifying trimming
	  of exons at ends.

2006-11-01 06:27  twu

	* src/except.c: Stopping deletion of global_except_key, because
	  worker threads may still need it

2006-11-01 06:27  twu

	* src/blackboard.c: Letting each thread destroy its own reqpost

2006-10-31 01:47  twu

	* src/gmap.c: Added -Y flag for performing strict translation of
	  cDNA sequence.  Removed worker_assignments variable, and using
	  global blackboard variable instead to handle exceptions.

2006-10-31 01:45  twu

	* src/: stage3.c, stage3.h, translation.c, translation.h: Added
	  strictp flag for protein translation

2006-10-31 01:44  twu

	* src/oligoindex.c: Dropped oligospace requirements for PMAP by
	  reducing amino acid alphabet in stage 2 from 20 to 16.

2006-10-31 01:43  twu

	* src/: gmapindex.c, pmapindex.c, indexdb.c: Fixed memory
	  allocation for filename

2006-10-31 01:43  twu

	* src/except.c: Fixed location of compiler directive

2006-10-31 01:42  twu

	* src/blackboard.c: Put mutex locks outside of updates to input
	  counter and output counter.  This is to be cautious, since only
	  input thread and output thread, respectively, should be affecting
	  these counters.

2006-10-24 06:18  twu

	* src/stage3.c: Fixed undefine_nucleotides to handle gapholders

2006-10-24 06:18  twu

	* src/oligoindex.c: Using calloc instead of malloc for initializing
	  oligoindex space

2006-10-24 06:17  twu

	* src/gmap.c: Reduced indexsizes in PMAP, so they won't overflow in
	  some machines

2006-10-24 06:15  twu

	* src/backtranslation.c: Fixed usage of translation_start and
	  translation_end

2006-10-20 01:14  twu

	* src/gmap.c: Printing messages to stderr when no paths are found,
	  in all cases where sequence headers are not printed.

2006-10-20 01:13  twu

	* src/translation.c: Fixed coordinates for translation start and
	  end

2006-10-20 01:13  twu

	* src/stage3.c: Fixed bug with NULL path passed to
	  undefine_nucleotides

2006-10-20 01:12  twu

	* src/pair.c: Changed gff3 procedures to treat translation start
	  and end values as query positions, not alignment indices.

2006-10-16 01:53  twu

	* src/stage3.c: Making sure that gaps are inserted after smoothing
	  procedure deletes exons

2006-10-16 01:52  twu

	* src/stage2.c: Clarified differences between amino acid indexsize
	  and nucleotide indexsize.  Cleaned up code for filling in
	  oligomers.

2006-10-16 01:51  twu

	* src/smooth.c: Reduced definition of a gap between exons

2006-10-16 01:51  twu

	* src/oligop.c: Included possibility of 12-amino acid alphabet for
	  8-mers.

2006-10-16 01:50  twu

	* src/indexdb.h: Included possibility of 12-amino acid alphabet for
	  8-mers.  Provided compile-time values for file suffixes.

2006-10-16 01:50  twu

	* src/indexdb.c: Included possibility of 12-amino acid alphabet for
	  8-mers

2006-10-16 01:49  twu

	* src/pmapindex.c: Performing complete build with a single command

2006-10-16 01:49  twu

	* src/gmapindex.c: Using compiler-time value for suffix

2006-10-16 01:48  twu

	* src/gmap.c: Printing value of INDEX1PART in help output for PMAP

2006-10-13 03:56  twu

	* tests/align.test.ok: Fixed coordinate to match corrected version
	  of program

2006-10-13 03:42  twu

	* src/oligoindex.c: Added debugging statements

2006-10-13 03:29  twu

	* src/translation.c: Fixed bug with translating cDNA beyond the
	  genomic stop

2006-10-13 03:02  twu

	* src/stage3.c: Reorganized passes through the alignment.  Made
	  peelback routines more robust.

2006-10-13 02:57  twu

	* src/smooth.h: Using stage 2 indexsize in smoothing procedures

2006-10-13 02:56  twu

	* src/smooth.c: Major rewrite of smoothing procedures

2006-10-13 02:51  twu

	* src/dynprog.c: Added another mechanism to prevent microexon from
	  having a gap at either end

2006-10-12 02:31  twu

	* src/gmap.c: Allowing "-t 0" to mean non-threaded behavior.  Using
	  new thread-safe exception handler.

2006-10-12 02:30  twu

	* src/: dynprog.c, dynprog.h: Fixed traceback for cDNA gaps

2006-10-12 02:30  twu

	* src/: except.c, except.h: Re-implemented thread-safe exception
	  handler to remove memory leaks.  Now using exception frames in
	  stack rather than in heap.

2006-10-12 02:28  twu

	* src/stage3.c: Fixed peelback to codon boundaries for PMAP.
	  Relaxed forcep requirement for single gaps.  Recognizing cases
	  where prior genome or cDNA gap solution was obtained.

2006-10-12 02:26  twu

	* src/stage3.h: Removed ngap from parameter lists when possible

2006-10-12 02:24  twu

	* src/stage1.c: Initialized a diagnostic variable

2006-10-12 02:24  twu

	* src/: pair.c, pair.h: Removed unused code and variables

2006-10-11 04:16  twu

	* src/: except.c, except.h: Implemented thread-safe version of
	  exception handler

2006-10-11 02:37  twu

	* src/gmap.c: Added -j flag to control printing of dual breaks

2006-10-11 02:36  twu

	* src/: except.c, except.h: Reformatted exception handling code.
	  Using pointers to frames.

2006-10-10 10:12  twu

	* src/: stage3.c, stage3.h: Rewrote peelback routines.	More
	  accurate handling of coordinates and checking of coordinates and
	  gaps.

2006-10-10 10:10  twu

	* src/dynprog.c: Advancing query and genome coordinates in cases of
	  skips

2006-10-10 10:09  twu

	* src/smooth.c: Revised trimming at ends to use individual exons,
	  rather than the sum of exon and intron lengths

2006-10-10 10:08  twu

	* src/pairpool.c: Showing pointer to pair in debugging statements

2006-10-10 10:08  twu

	* src/pair.c: Showing queryjump and genomejump in debugging
	  statements

2006-10-10 10:08  twu

	* src/gmap.c: Added -0 flag to inactivate exception handler, and -7
	  and -8 flags to show results of stage 2 and smoothing,
	  respectively.

2006-10-10 10:07  twu

	* src/: except.c, except.h: Added mechanism to inactivate exception
	  handler

2006-10-09 03:02  twu

	* src/access.c: Fixed compiler warning about reference to void *.

2006-10-09 03:02  twu

	* src/: chimera.c, block.c: Removed unused variables

2006-10-09 03:01  twu

	* src/genome.c: Fixed compiler warning about mismatched variable
	  types.

2006-10-09 03:01  twu

	* src/gmap.c: Added flag for pruning level.  Inactivated conversion
	  of signals to exceptions with diagnostic flag.  Removed
	  references to badoligos.

2006-10-09 03:00  twu

	* src/indexdb.c: Added necessary header file.  Fixed compiler
	  warning about mismatched variable types.

2006-10-09 02:59  twu

	* src/: intron.c, genome-write.c, dynprog.c, compress.c: Added
	  necessary header file

2006-10-09 02:59  twu

	* src/matchpool.h: Added declarations of external functions

2006-10-09 02:58  twu

	* src/: oligoindex.c, oligoindex.h: Computing estimate of
	  maxconsecutive when mappings are obtained

2006-10-09 02:58  twu

	* src/: pair.c, pair.h: Added diagnostic information about stage 2
	  maxconsecutive.

2006-10-09 02:58  twu

	* src/: result.c, result.h: Added diagnostic information about
	  initial query check

2006-10-09 02:57  twu

	* src/smooth.c: Handling possible gaps at ends of alignment

2006-10-09 02:56  twu

	* src/stage2.c: Using maxconsecutive estimate from
	  Oligoindex_get_mappings to determine whether to proceed with
	  stage 2.

2006-10-09 02:56  twu

	* src/: stage1.c, sequence.c, oligo.c: Removed unused variables

2006-10-09 02:55  twu

	* src/stage3.c: Added diagnostic information about stage 2
	  maxconsecutive.  Fixed procedure for removing adjacent dynamic
	  programming to remove all gaps, and then to reinsert them later.

2006-10-06 07:50  twu

	* src/: oligoindex.c, oligoindex.h: Added counting of replicate
	  oligos

2006-10-06 03:28  twu

	* util/md_coords.pl.in: Added information about number of contigs
	  in each strain

2006-10-06 03:27  twu

	* configure.ac: Removed obsolete tests.  Fixed problem in setting
	  share directory.  Added maintainer option.

2006-10-06 03:26  twu

	* MAINTAINER: Added reminder to check that files are current in CVS

2006-10-06 03:26  twu

	* src/gmap.c: Distinguishing between poor and repetitive sequences.
	  Providing -p flag to control pruning behavior.

2006-10-06 03:24  twu

	* src/result.h: Distinguishing between poor and repetitive
	  sequences

2006-10-06 03:24  twu

	* src/sequence.c: Set skiplength correctly on empty sequences

2006-10-06 02:08  twu

	* src/gmap.c: Added -W flag to force GMAP to compute repetitive or
	  poor sequences

2006-10-06 02:07  twu

	* src/oligoindex.c: Limited definition of badoligo to consider only
	  non-ACGT characters, and not to consider number of hits.

2006-10-06 01:41  twu

	* src/stage3.c: Fixed bug arising from gaps left at ends of
	  alignment

2006-10-06 01:40  twu

	* src/dynprog.c: Disallowing bridges of introns and cDNA insertions
	  that lead to coordinate errors

2006-10-06 01:39  twu

	* src/gmap.c: Changed thread-based exception handling to kill all
	  other threads and to report all worker assignments

2006-10-05 12:25  twu

	* src/stage3.h: Made checking of coordinates occur in diagnostic
	  mode.

2006-10-05 12:25  twu

	* src/stage3.c: Made checking of coordinates occur in diagnostic
	  mode.  Fixed case where cDNA gap turned into a single gap after
	  peelback.

2006-10-05 12:24  twu

	* src/stage1.c: Fixed memory leak

2006-10-05 12:23  twu

	* src/smooth.c: Fixed bug resulting from apparent negative exon and
	  negative intron lengths.

2006-10-05 12:23  twu

	* src/oligoindex.c: Restored pruning of sequences with bad oligos.

2006-10-05 12:22  twu

	* src/gmap.c: Added handlers to convert signals into exceptions, to
	  indicate the problematic sequence.  Restored pruning of sequences
	  with bad oligos.

2006-10-04 11:53  twu

	* src/: result.c, stage1.c, stage1.h: Added reporting of more
	  diagnostic information

2006-10-04 11:52  twu

	* src/stage2.c: Fixed problems with uninitialized variable

2006-10-04 11:52  twu

	* src/matchpair.c: Fixed problem with uninitialized variable

2006-10-04 05:30  twu

	* src/access.c: Using a Stopwatch_T object

2006-10-04 05:30  twu

	* src/: stage1.c, stage1.h, stage2.c, stage2.h, stage3.c, stage3.h:
	  Storing diagnostic information

2006-10-04 05:29  twu

	* src/: result.c, result.h, gmap.c: Printing diagnostic information
	  upon request

2006-10-04 05:29  twu

	* src/smooth.c: Fixed memory leak

2006-10-04 05:26  twu

	* src/: pair.c, pair.h: Printing diagnostic information upon
	  request

2006-10-04 05:26  twu

	* src/oligoindex.c: Stopped initializing data buffer for
	  Oligoindex_T object

2006-10-04 05:24  twu

	* src/: stopwatch.c, stopwatch.h: Created a Stopwatch_T object

2006-10-03 10:41  twu

	* src/stage3.c: Removed unnecessary list reversal

2006-10-03 10:40  twu

	* src/pair.c: Allowing jump in querypos in pair check procedure

2006-10-02 11:02  twu

	* src/gmap.c: Provide stage 2 information in diagnostic output.
	  Use stage 2 information to prune bad alignments before stage 3.

2006-10-02 11:01  twu

	* src/stage3.c: Provide stage 2 information in diagnostic output.
	  Allow a single open in scoring a single intron compared with dual
	  introns.

2006-10-02 11:00  twu

	* src/stage2.h: Interface provides number of canonical and
	  non-canonical introns

2006-10-02 11:00  twu

	* src/stage2.c: Returned to using gendistance for computing
	  penalties, except for diffdistance in deadp.	Fixed bug in
	  tallying unknown types of introns.

2006-10-02 10:58  twu

	* src/sequence.c: Fixed problems with reading control-M characters
	  (PC line feed) in input.

2006-10-02 10:57  twu

	* src/pair.h: Reporting stage 2 information in diagnostic output.

2006-10-02 10:57  twu

	* src/pair.c: Reporting stage 2 information in diagnostic output.
	  Counting indels in computing percent identity for each exon.

2006-10-02 10:57  twu

	* src/dynprog.c: Eliminated extra reward for finding semicanonical
	  introns in final pass

2006-10-02 02:21  twu

	* src/stage2.c: Need to take abs() when measuring diffdistance.
	  Scoring behavior checked against revision 1.157.  Making stage2
	  information available for diagnostic output.

2006-09-30 13:55  twu

	* src/gmap.c: Added -8 flag to show results of stage 2 calculation

2006-09-30 13:55  twu

	* src/boyer-moore.c: Revised procedure to handle ambiguous
	  characters for PMAP.

2006-09-30 13:55  twu

	* src/dynprog.h: Added dynprogindex information.

2006-09-30 13:54  twu

	* src/dynprog.c: Added table for performing Boyer-Moore searches of
	  microexons for PMAP.	Reduced penalties for extending gaps.
	  Added separate rewards for final pass of finding canonical
	  introns.  Added dynprogindex information.

2006-09-30 13:51  twu

	* src/smooth.c: Systematically checking ends for smoothing.  Using
	  matches instead of lengths to evaluate exons.  Added
	  probabilistic checking for marking middle exons.

2006-09-30 13:50  twu

	* src/stage3.h: Passing stage2p as a parameter to Stage3_compute.

2006-09-30 13:49  twu

	* src/stage3.c: Major changes to algorithm.  Added iteration
	  through smoothing, dual intron, and single intron passes.
	  Checking peel back to determine if canonical intron needs to be
	  recomputed.  Added final pass to find introns with higher reward.
	  Added dynprogindex information.  Using dynprogindex information
	  in peeling leftward and rightward.

2006-09-30 13:44  twu

	* src/stage1.c: New criterion for setting usep to false, namely, if
	  support is less than a certain fraction of the maximum observed
	  support.

2006-09-30 13:43  twu

	* src/pair.h: Pair_check_array now returns a bool.

2006-09-30 13:43  twu

	* src/pair.c: Handling more cases of short gaps as indels.
	  Printing dynprogindex in diagnostic and debugging output.

2006-09-30 13:38  twu

	* src/stage2.c: Reverted to algorithm from revision 1.157.  Using
	  diffdistance instead of gendistance.	Making sufflookback depend
	  on mapfraction.

2006-09-28 10:59  twu

	* src/stage2.c: Changes made to scoring algorithm, but not
	  well-motivated.  Fixed bugs in predicting cDNA direction.

2006-09-18 14:52  twu

	* src/stage3.c: Fixed bug when recomputing over adjacent dynamic
	  programming regions at end of sequence

2006-09-18 14:51  twu

	* src/stage2.c: Revised rules for giving credit for query distance,
	  giving none if difference in distance is greater than min intron
	  length.

2006-09-18 14:47  twu

	* src/stage1.c: Doubling genomic region with each iteration, until
	  sufficient support found for a matchpair.

2006-09-18 14:44  twu

	* src/: matchpair.c, matchpair.h: Computing and storing fraction of
	  stage 1 support

2006-09-18 14:43  twu

	* src/: gbuffer.c, gbuffer.h, gmap.c: Allowed Genome_T object to
	  exceed default length of genomic segment

2006-09-18 14:42  twu

	* src/dynprog.c: Reduced penalties for gap extension, to match
	  reductions in mismatch penalties

2006-09-18 14:41  twu

	* src/Makefile.am: Provided target machine during compilation

2006-09-11 09:01  twu

	* src/gmap.c: Included build target in version output.	Increased
	  oligomer size in PMAP from 3-4 to 4-5.

2006-09-08 06:30  twu

	* src/stage2.c: Added oligos to output of debugging statements

2006-09-08 05:26  twu

	* configure.ac: Using AC_FUNC_FSEEKO to check for fseeko.  Added
	  comment line for $Id$.

2006-09-07 10:31  twu

	* src/stage2.c: Added debugging statements for finding shifted
	  canonical introns

2006-09-07 10:30  twu

	* src/stage1.c: Increased trimlength and extension past ends for
	  PMAP

2006-09-07 10:29  twu

	* src/gmap.c: Increased maxextension to 120000

2006-09-01 09:07  twu

	* src/translation.c: Making sure to assign values to variables when
	  number of alignment pairs is fewer than the minimum

2006-09-01 09:06  twu

	* src/pair.c: Fixed bug in printing CDS of GFF3 format

2006-09-01 05:12  twu

	* src/stage3.c: For PMAP, trimming ends of alignment to codon
	  boundaries

2006-09-01 05:11  twu

	* src/translation.c: Removed check for minimum number of pairs for
	  PMAP

2006-09-01 04:42  twu

	* src/dynprog.c: Changed calls to Pairpool_push.  Added
	  dynprogindex information.  Reduced penalty for mismatches.

2006-09-01 04:42  twu

	* src/dynprog.h: Changed calls to Pairpool_push.  Added
	  dynprogindex information.

2006-09-01 04:41  twu

	* src/stage3.c: Fixed bug where peeling back yielded wrong
	  coordinates.	Changed calls to Pairpool_push.  Added dynprogindex
	  information.	Recomputing regions with adjacent dynamic
	  programming solutions.

2006-09-01 04:39  twu

	* src/: stage2.c, matchpair.c: Changed calls to Pairpool_push

2006-09-01 04:38  twu

	* src/smooth.c: Added debugging statements for exon and intron
	  lengths

2006-09-01 04:38  twu

	* src/sequence.c: Fixed bug where return type should be int, not
	  bool.

2006-09-01 04:38  twu

	* src/: pairpool.c, pairpool.h: Distinguished between gapholder and
	  gapalign elements.  Added dynprogindex to Pairpool_push.

2006-09-01 04:37  twu

	* src/pair.c: Added debugging option for printing dynprogindex

2006-09-01 04:37  twu

	* src/pairdef.h: Added dynprogindex to struct.	Reordered fields.

2006-09-01 04:36  twu

	* src/bool.h: Defining bool to be an unsigned char instead of an
	  enumerated type

2006-08-03 07:24  twu

	* tests/: align.test.ok, map.test.ok: Changed output for coverage
	  to use bp instead of nt

2006-08-03 07:15  twu

	* util/fa_coords.pl.in: Added pattern Chr_ seen in some TIGR
	  genomes.  Changed variable name from chronlyp to concatenatedp.

2006-08-03 07:13  twu

	* src/oligoindex.c: Added check for query lengths shorter than
	  index size

2006-08-03 07:12  twu

	* src/: iit-read.c, iit-read.h, iit_dump.c: Added option to dump
	  counts of each segment

2006-08-03 07:11  twu

	* src/: get-genome.c, iit_get.c: Allowed program to take coordinate
	  requests from stdin

2006-08-03 07:09  twu

	* src/gmap.c: Printing calling arguments in gff mode

2006-06-12 04:51  twu

	* src/stage3.c: Turned off gap checking

2006-06-12 04:50  twu

	* src/pair.c, util/gmap_compress.pl.in, util/gmap_uncompress.pl.in:
	  Using bp to denote query length, instead of nt

2006-06-12 04:45  twu

	* configure.ac: Consolidated tests.  Added a maintainer flag.

2006-06-12 04:45  twu

	* config.site.gne: Enabled maintainer flag

2006-06-12 04:44  twu

	* tests/setup1.test.in: Using correct directories.  Consolidated
	  several tests into this one.

2006-06-12 04:44  twu

	* tests/: align.test.in, coords1.test.in: Using correct directories

2006-06-12 04:43  twu

	* tests/Makefile.am: Putting all temporary files into a
	  subdirectory

2006-06-12 04:42  twu

	* tests/defs: Initial import into CVS

2006-06-12 04:42  twu

	* util/gmap_compress.pl.in: Putting cDNA length into the Coverage
	  field

2006-06-12 04:40  twu

	* util/gmap_uncompress.pl.in: Getting cDNA length from the Coverage
	  field

2006-05-31 04:04  twu

	* src/: params.c, params.h: Adding maxoligohits as a parameter

2006-05-31 04:03  twu

	* src/: oligoindex.c, oligoindex.h: Using maxoligohits parameter,
	  and reducing it for cross-species alignment (to avoid random and
	  misleading matches)

2006-05-31 04:03  twu

	* src/stage2.h: Using maxoligohits parameter

2006-05-31 04:02  twu

	* src/stage2.c: For cross-species alignment, increasing
	  enough_consecutive parameter and not opportunistically
	  increasingly sampling interval

2006-05-31 04:01  twu

	* src/stage1.h: Reduced SINGLEINTRONLENGTH to 100000

2006-05-31 04:01  twu

	* src/stage1.c: Using maxextension parameter instead of
	  SINGLEINTRONLENGTH directly

2006-05-31 04:00  twu

	* src/gmap.c: Limited crossspecies parameters to maxextension and
	  maxoligohits.

2006-05-25 09:30  twu

	* src/stage2.c: Introduced detection of semicanonical introns and
	  penalty for these.  Removed distpenalty_dead, and introduced
	  distpenalty_noncanonical; motivated by ENST0356720.  Decreased
	  distpenalty; motivated by ENST0356222.  Introduced procedure for
	  querydist_credit, bounded below by zero.  Decreated querydist
	  points when gendistance equals querydistance; motivated by
	  ENST0354988.

2006-05-25 09:22  twu

	* src/gmap.c: Using single intron length as basis for maxextension

2006-05-25 09:22  twu

	* src/stage3.c: Made initial pass of build_pairs_singles work only
	  when genomejump equals queryjump; motivated by ENST0341339.  Made
	  acceptable mismatches for dual introns depend again on defect
	  rate.

2006-05-25 09:18  twu

	* src/smooth.c: Removed deletion of longest middle exon in a series
	  of short exons.  Motivated by ENST0348697.

2006-05-25 09:17  twu

	* src/: stage1.c, stage1.h: Using single intron length to extend
	  genomic segment at ends.  Motivated by ENST0358972.

2006-05-25 09:15  twu

	* src/oligoindex.c: Increased thetadiff for trimming repetitive
	  oligos from 2 to 20.	Motivated by ENST0357282.

2006-05-25 09:14  twu

	* src/: gbuffer.c, gbuffer.h: Added data structures for storing
	  positions of semicanonical dinucleotides

2006-05-25 09:12  twu

	* src/: dynprog.c, dynprog.h: Made microexon p-value threshold
	  depend on the defect rate.  Increased genomejump needed for
	  single gap penalties to apply.  Motivated by ENST0262608.

2006-05-23 07:33  twu

	* tests/map.test.in: Incorporated into setup1.test.in

2006-05-23 07:26  twu

	* tests/: iit_dump.test.in, iit_get.test.in: Incorporated into a
	  single iit test script

2006-05-23 07:26  twu

	* tests/iit_store.test.in: Renamed to iit.test.in

2006-05-23 07:24  twu

	* tests/: iit.test.in, iit_store.test.in: Made script run in a
	  subdirectory.  Combined iit_store, iit_get, and iit_dump tests
	  into one script.

2006-05-22 17:12  twu

	* src/stage2.c: Moved preprocessor directive outside of macro
	  (needed for gcc3 compiler).

2006-05-22 16:43  twu

	* src/: gmap.c, stage3.c, stage3.h: Changed variable name from
	  extend_mismatch_p to trimalignmentp

2006-05-22 16:42  twu

	* src/changepoint.c: Changed criterion from a differences in theta
	  to a ratio

2006-05-19 07:47  twu

	* share/: archive.html, index.html: Made changes to reflect
	  2006-05-19 version

2006-05-19 07:47  twu

	* VERSION: Updated version

2006-05-19 07:46  twu

	* tests/: align.test.ok, map.test.ok: Changed answers to reflect
	  new output format

2006-05-19 07:39  twu

	* src/stage3.c: Removed trimming of alignments in PMAP

2006-05-19 07:38  twu

	* src/stage1.c: Changed some parameters to increase sensitivity

2006-05-19 07:36  twu

	* src/: chrsubset.c, chrsubset.h: Added function Chrsubset_make

2006-05-19 03:15  twu

	* src/translation.c: Fixed assignment of amino acids to genomic
	  sequence in PMAP

2006-05-19 03:15  twu

	* src/stage3.h: Minor formatting change

2006-05-19 03:15  twu

	* src/stage3.c: Printing trimmed query coordinates in path summary.
	  Pruning stage 3 result of coverage is less than MINCOVERAGE.

2006-05-19 03:14  twu

	* src/sequence.h: Added appropriate MAXSEQLEN for PMAP

2006-05-19 03:14  twu

	* src/: reader.c, reader.h: Allowing reading in each direction to
	  proceed to the ends of the query sequence

2006-05-19 03:13  twu

	* src/pairpool.c: Setting initial value for aa_g and aa_e

2006-05-19 03:13  twu

	* src/: pair.c, pair.h: Printing trimmed query coordinates in path
	  summary

2006-05-19 03:12  twu

	* src/oligoindex.c: Reinstated trimming of query sequence based on
	  changepoint analysis

2006-05-19 03:12  twu

	* src/mem.c: Fixed compiler warning about pointer arithmetic on
	  void *.

2006-05-19 03:11  twu

	* src/matchpair.c: Added comments

2006-05-19 03:11  twu

	* src/gmap.c: Performing trimming of query sequence in more cases.
	  Changed name of "mutation reference" to "reference sequence".

2006-05-19 03:10  twu

	* src/dynprog.c: Removed step function penalty based on codons.
	  Reduced extension penalty to obtain better behavior.

2006-05-19 03:09  twu

	* src/stage2.c: Changed position for starting to compute mismatch
	  gaps.  Added trimming at ends for PMAP.

2006-05-19 03:07  twu

	* src/stage1.c: Improved calculation of genome segment length,
	  based on expected exon and intron sizes.  In sampling mode,
	  continuing sampling at current position of block pointers.

2006-05-19 03:06  twu

	* src/: block.c, block.h: Added procedures for saving and restoring
	  blocks

2006-05-19 02:50  twu

	* share/: archive.html, index.html: Web pages as of 2006-04-21

2006-05-15 13:49  twu

	* src/: Makefile.am, gbuffer.c, gbuffer.h, gmap.c, matchpair.c,
	  matchpair.h, pair.c, pair.h, stage2.c, stage2.h, stage3.c,
	  stage3.h: Created Gbuffer_T object to use as workspace for
	  various calculations

2006-05-15 07:11  twu

	* src/translation.c: Fixed uninitialized variable

2006-05-15 07:10  twu

	* src/: dynprog.c, pair.c: Made cDNA gaps into type SHORTGAP_COMP
	  instead of INDEL_COMP, so they get treated properly by the
	  changepoint analysis

2006-05-15 07:09  twu

	* src/stage3.c: Fixed memory leak

2006-05-15 07:09  twu

	* src/changepoint.c: Changed changepoint parameters slightly

2006-05-13 17:13  twu

	* src/stage3.c: Added checks to make sure both qgenome lengths are
	  adequately long in dual intron gaps

2006-05-13 17:12  twu

	* src/dynprog.c: Increased penalties for mismatches

2006-05-13 17:11  twu

	* src/gmap.c: Changed 'U' flag to mean no trimming of poor
	  alignments at ends

2006-05-13 12:24  twu

	* src/gmap.c: Changed interfaces to some Stage3_T functions

2006-05-13 12:24  twu

	* src/: pair.c, pair.h: Added query length to Coverage line

2006-05-13 12:24  twu

	* src/stage1.c: Fixed bug where maxtrial wasn't set

2006-05-13 12:23  twu

	* src/stage2.c: Removed final assignment of dinucleotide positions

2006-05-13 12:23  twu

	* src/stage3.h: Changed some interfaces to Pair_T functions

2006-05-13 12:23  twu

	* src/stage3.c: Added some shortcuts for changepoint analysis.
	  Changed some interfaces to Pair_T functions.

2006-05-12 15:47  twu

	* src/gmap.c: Provided initial values to some variables

2006-05-12 15:47  twu

	* src/oligoindex.c: Reduced MAXHITS parameter from 200 to 20

2006-05-12 15:46  twu

	* src/stage1.c: Limiting trials for same-species alignment.
	  Limiting salvage algorithm to short sequences and cross-species
	  alignment.

2006-05-12 15:44  twu

	* src/stage2.c: Implemented faster method for finding shifted
	  canonical introns

2006-05-12 12:07  twu

	* src/stage2.c: Saving mappings for each indexsize, and going back
	  to best one.	Introduced idea of sufficient and minimum map
	  fraction, and aborting if minimum map fraction not satisfied.

2006-05-12 04:36  twu

	* src/: gmap.c, stage3.c, stage3.h: Added option to print output in
	  IIT FASTA map format

2006-05-12 04:36  twu

	* src/: pair.c, pair.h: Removed parameter from Pair_print_iit_map

2006-05-12 04:25  twu

	* src/: pair.c, pair.h: Removed old code.  Added a procedure for
	  printing an IIT map.

2006-05-12 04:09  twu

	* src/sequence.c: Removed printing of '>' from
	  Sequence_print_header

2006-05-12 03:49  twu

	* src/iit-read.c: Fixed bug in printing results from map iit

2006-05-12 03:46  twu

	* src/stage2.c: Added debugging statements

2006-05-11 05:35  twu

	* src/: gmap.c, pair.c, pair.h, stage3.c, stage3.h: Included
	  filename of user-provided genomic seg as source in gff3 output

2006-05-11 05:35  twu

	* src/iit_dump.c: Included header for getopt_long

2006-05-11 04:54  twu

	* README: Added more information about IIT utilities

2006-05-11 04:46  twu

	* src/: iit-read.c, iit-read.h: Added annotation-only option to
	  IIT_dump

2006-05-11 04:46  twu

	* src/get-genome.c: Changed program description statement slightly

2006-05-11 04:46  twu

	* src/: Makefile.am, iit_dump.c, iit_get.c, iit_store.c: Added long
	  options and documentation for the IIT utilities

2006-05-11 03:26  twu

	* src/iit_store.c: Added support for quotation marks in gff3
	  features

2006-05-11 03:14  twu

	* src/: chrnum.c, chrnum.h, chrsubset.c: Using new Chrnum_to_string
	  interface

2006-05-11 03:14  twu

	* src/: gmap.c, stage3.c, stage3.h: Added cDNA_match option for
	  gff3 output

2006-05-11 03:13  twu

	* src/: pair.c, pair.h: Added cDNA_match option for gff3 output,
	  including Gap attribute.  Using new Chrnum_to_string interface.

2006-05-10 23:32  twu

	* src/: gmap.c, params.c, params.h, stage3.c, stage3.h: Added
	  procedures for allowing chromosome-tagged IIT map files, in
	  addition to strand-tagged IIT map files.

2006-05-10 23:26  twu

	* src/: iit-read.c, iit-read.h: Added functions for retrieving
	  multiple types and for getting label when access mode is fileio.

2006-05-10 16:53  twu

	* src/iit_get.c: Allowing user to specify multiple types

2006-05-10 16:52  twu

	* src/iit_store.c: Modified gff3 parsing to assign only one tag for
	  each row.  Using feature column as a source for labels.

2006-05-10 10:44  twu

	* src/: pair.c, pair.h: Added routines for output in GFF3 format

2006-05-10 10:44  twu

	* src/Makefile.am: Added trimming of alignment based on changepoint
	  analysis

2006-05-10 10:21  twu

	* src/stage2.c: Fixed bug in scanning for reverse canonical intron

2006-05-10 10:11  twu

	* src/gmap.c: Added flags for gff3 output

2006-05-10 10:11  twu

	* src/: translation.c, backtranslation.c, pairdef.h, pairpool.c:
	  Introduced phase

2006-05-10 10:10  twu

	* src/: stage3.c, stage3.h: Added procedure for trimming pairs.
	  Added gap when bounds don't make sense for dual intron gaps.
	  Introduced gff3 format and phase.

2006-05-10 10:08  twu

	* src/: changepoint.c, changepoint.h: Initial import into CVS

2006-05-10 02:17  twu

	* src/stage2.c: Added debugging statements for the result of stage
	  2 prior to trimming

2006-05-10 02:05  twu

	* src/: pair.c, pair.h: Added a function for computing matchscores
	  from an alignment

2006-05-10 02:05  twu

	* src/dynprog.c: Changed various gap penalties, especially at ends
	  of sequence

2006-05-10 01:57  twu

	* src/iit_get.c: Changed atol() to strtoul(), because atol() was
	  truncating numbers above 2^31 in machines with long ints of 4
	  bytes.

2006-05-08 07:49  twu

	* src/stage2.c: Changed condition for re-computing dead links from
	  an "or" to an "and" on both directions.  Added trimming of ends,
	  based on consecutive matches.

2006-05-07 06:03  twu

	* src/stage2.c: Cleaned up procedure for finding introns in PMAP,
	  which can be shifted.  Cleaned up counts of canonical and total
	  introns.

2006-05-07 06:01  twu

	* src/stage3.c: Fixed problems with shortcut for existing introns
	  and with coordinates for dual genome pairs

2006-05-07 05:59  twu

	* src/oligoindex.c: Added debugging statement

2006-05-06 10:47  twu

	* src/stage2.c: Reworking of stage 2 scoring to make it more robust
	  for low-identity sequences.  Includes identification of possible
	  canonical sites by shifting boundaries.

2006-05-06 02:09  twu

	* src/: stage3.c, stage3.h: Using dynamic programming paths
	  computed for dual intron gaps

2006-05-06 02:08  twu

	* src/: gmap.c, stage2.c, stage2.h: Computing indexsize adaptively

2006-05-06 02:06  twu

	* src/: smooth.c, smooth.h: Removed indexsize from smoothing
	  procedures

2006-05-06 02:06  twu

	* src/: params.c, params.h: Added minindexsize and maxindexsize to
	  params

2006-05-06 02:00  twu

	* src/: oligoindex.c, oligoindex.h: Changed PMAP indexsize to be in
	  aa.  Calculating mapfraction.

2006-05-05 17:44  twu

	* src/pair.c: Keeping ambiguous character and comp in PMAP
	  alignments

2006-05-05 17:43  twu

	* src/: intron.c, intron.h: Added function to return string for
	  printing intron type

2006-05-05 17:42  twu

	* src/: gmap.c, oligoindex.c, oligoindex.h: Put indexsize
	  parameters inside of Oligoindex_T object

2006-05-05 03:41  twu

	* util/md_coords.pl.in: Improved handling of alternate strains

2006-05-04 09:32  twu

	* src/iit_store.c: Implemented parsing of gff format

2006-05-04 09:31  twu

	* src/gmap.c: Incremented stuttercycles for PMAP

2006-05-04 09:30  twu

	* src/indexdb.c: In monitoring commands, printing positions with
	  commas

2006-05-04 09:30  twu

	* src/: matchpair.c, matchpair.h, stage1.c: Using maxintronlen
	  instead of querylen as criterion for removing hits before
	  clustering

2006-05-04 09:28  twu

	* src/stage2.c: Checking two possible query positions for intron in
	  PMAP

2006-05-04 09:28  twu

	* src/: dynprog.c, dynprog.h: Removed obsolete parameters for
	  computing genome gaps

2006-05-04 09:27  twu

	* src/stage3.c: Fixed boundaries for check of dual introns

2006-05-04 06:12  twu

	* util/fa_coords.pl.in: Improved monitoring messages to indicate
	  when coordinates are parsed and when they are concatenated.

2006-05-04 06:11  twu

	* util/md_coords.pl.in: Fixed bug in handling alternate strains

2006-05-02 18:12  twu

	* src/: md5-compute.c, oligo-count.c: Using new version of
	  Sequence_read

2006-05-02 02:04  twu

	* src/stage2.c: Removed statement that does not apply to PMAP

2006-05-02 02:02  twu

	* src/matchpair.c: Fixed computation of support for PMAP.  Added
	  debugging statements

2006-05-02 02:02  twu

	* src/match.c: Fixed genomic segment retrieved for debugging

2006-05-02 01:59  twu

	* src/iit-read.c: Minor editing changes

2006-05-02 01:58  twu

	* src/datadir.c: Improved error message when genome directory isn't
	  found

2006-05-02 01:58  twu

	* src/compress.c: Removing spaces from reading of uncompressed
	  sequence

2006-05-02 01:57  twu

	* src/stage1.c: Increased matchpairs allowed.  Fixed position
	  adjustment for reverse strand matches on PMAP.

2006-05-02 01:56  twu

	* src/indexdb.c: Shifted positions for .prxpositions down by one.

2006-04-21 02:38  twu

	* VERSION: Updated version

2006-04-21 02:37  twu

	* util/gmap_setup.pl.in: Fixed bugs in printing of instructions

2006-04-21 02:37  twu

	* util/fa_coords.pl.in: Augmented patterns allowed for specifying
	  chromosomal location of contigs

2006-04-21 02:36  twu

	* src/: Makefile.am, chrsubset.c, chrsubset.h, get-genome.c: Added
	  ability to print all chromosomal subsets from get-genome

2006-04-21 02:36  twu

	* src/datadir.c: Improved error message

2006-04-21 02:07  twu

	* README: Added information about the -q flag.	Added additional
	  forms for specifying chromosomal location of contigs.

2006-04-18 02:37  twu

	* util/gmap_setup.pl.in: Added the -q and -Q flags for specifying
	  indexing intervals

2006-04-07 06:25  twu

	* util/gmap_setup.pl.in: Fixed bugs with new install statements

2006-04-07 06:25  twu

	* tests/align.test.ok: Changed gold standard to contain intron
	  lengths

2006-04-07 03:07  twu

	* VERSION: Updated version

2006-04-07 03:06  twu

	* util/gmap_setup.pl.in: Added comment about editing .chrsubset
	  file.  Creating genome.maps directory.

2006-04-07 03:06  twu

	* src/stage3.c: Turned off CHECK

2006-04-07 03:05  twu

	* README: Added comment about editing .chrsubset file

2006-04-07 03:05  twu

	* MAINTAINER: Added check for CHECK

2006-04-06 11:25  twu

	* util/gmap_compress.pl.in: Changed program to handle intron
	  lengths in exon summary

2006-04-06 11:21  twu

	* src/: stage2.c, stage2.h: Introduced limit on individual intron
	  lengths

2006-04-06 11:21  twu

	* src/: stage1.c, stage1.h: Changed variable name from maxintronlen
	  to maxtotallen

2006-04-06 11:18  twu

	* src/gmap.c: Added separate flag for limiting individual intron
	  lengths

2006-04-06 11:17  twu

	* src/pair.c: Added intronlengths to exon summary

2006-04-06 09:20  twu

	* src/sequence.h: Increased maximum sequence length to be 1000000.

2006-04-04 09:22  twu

	* src/stage3.c: Building singles if a short exon is deleted during
	  smoothing

2006-04-04 09:21  twu

	* src/smooth.c: Improved debugging statements

2006-03-24 06:56  twu

	* tests/Makefile.am: Added INSTALL file to be cleaned up

2006-03-24 05:16  twu

	* util/gmap_setup.pl.in: Printing a copy of the install procedure
	  to a file

2006-03-24 03:05  twu

	* VERSION: Updated version

2006-03-20 10:03  twu

	* src/match.c: Match_npairings returns an int

2006-03-20 09:50  twu

	* tests/: setup2.test.in, setup1.test.in: Using new gmap_setup
	  procedure

2006-03-20 09:50  twu

	* tests/: coords1.test.in, coords1.test.ok, Makefile.am: Changed
	  names of files

2006-03-20 09:48  twu

	* util/md_coords.pl.in: Passing back maxwidth as a result.

2006-03-20 09:48  twu

	* src/gmap.c: Made changes for compatibility with PMAP.

2006-03-20 09:47  twu

	* src/: stage3.c, stage3.h: Giving maxpeelback information to
	  dynamic programming routine, so it can use single gap penalties
	  for long intron gaps.  Made changes for compatibility with PMAP.

2006-03-20 09:46  twu

	* src/: smooth.c, smooth.h: Changed smoothing routine to be based
	  on net intron lengths.  Sequences of small exons are removed if
	  they yield a net intron length of approximately zero.

2006-03-20 09:44  twu

	* src/: dynprog.c, dynprog.h: Disallowing intron or cDNA gaps to be
	  placed at the edge of the segment, which caused an error to occur
	  in the check_gaps routine.  Using single gap penalties for long
	  intron gaps.

2006-03-17 07:50  twu

	* src/sequence.c: Added handler for cases where requested
	  subsequence start and end are beyond the bounds of the sequence

2006-03-17 07:50  twu

	* src/: stage1.c, stage1.h, gmap.c: Added concept of maxtrial, to
	  be used for chimera (subsequence) problems

2006-03-17 07:49  twu

	* src/stage3.c: Added an exception handle for errors in checking
	  gaps

2006-03-17 07:48  twu

	* src/dynprog.c: Disallowed intron or cDNA gaps to be inserted at
	  ends of the subsequence, which results in an unexpected gap.

2006-03-05 13:46  twu

	* src/gmap.c: Providing maponlyp information to Sequence_read, to
	  turn skiplength warning message on or off.

2006-03-05 13:45  twu

	* src/sequence.h: Set MAXSEQLEN to be 200000

2006-03-05 13:43  twu

	* src/: stage3.c, pair.c: Revision of procedures to handle
	  sequences with skiplength

2006-03-05 13:42  twu

	* src/stage1.c: Expanded maxintronlen to include skiplength

2006-03-05 13:42  twu

	* src/: sequence.c, sequence.h: Addition of skiplength.  Rewriting
	  of code for reading sequences to handle skipping of middle
	  correctly.

2006-03-04 11:38  twu

	* src/gmap.c: Reworking of maponlyp case to generate a Stage3_T
	  object

2006-03-04 11:31  twu

	* src/: stage3.c, stage3.h: Implementedq Stage3_direct function for
	  maponlyp case.  Cleaned up merge function for combining two
	  Stage3_T objects.

2006-03-04 11:29  twu

	* src/: stage1.c, stage1.h: Cleaned up various procedures in stage
	  1 computation.  Simplified function identify_matches.
	  Eliminating extensions for maponlyp case.

2006-03-04 11:27  twu

	* src/: matchpair.c, matchpair.h: Added function for making a path
	  from a matchpair object

2006-03-04 11:26  twu

	* src/matchpool.c: Simplified code for handling positions on
	  reverse genomic strands.

2006-03-04 11:26  twu

	* src/: match.c, match.h: Added function for printing the oligomer
	  for a match.	Simplified code for handling positions on reverse
	  genomic strands.

2006-03-04 11:20  twu

	* src/oligoindex.c: Turned off code for changepoint analysis for
	  trimming ends

2006-03-04 11:16  twu

	* src/: pair.c, pair.h: Modified printing of path summary for
	  maponlyp

2006-03-04 11:15  twu

	* src/: result.c, result.h: Removed Stage1_T objects from Result_T

2006-03-04 11:14  twu

	* src/genome.c: Added debugging statements

2006-03-04 06:00  twu

	* src/: block.c, oligo.c, oligo.h: Fixed problem where oligomers
	  read from left side need to be shifted down to low 12-mer.  This
	  corrects problem with match coordinates being off by 4.

2006-03-02 06:53  twu

	* src/gmap.c: Revised code for computing chimeras

2006-03-02 06:52  twu

	* src/: chimera.c, chimera.h: Made Chimera_T object created only
	  when completely specified

2006-03-02 06:51  twu

	* src/stage3.c: Added a step to allow for subseq_offset, if present

2006-03-02 06:51  twu

	* src/: sequence.c, sequence.h: Added subseq_offset to Sequence_T

2006-03-01 10:23  twu

	* src/: dynprog.c, dynprog.h: Restored one gap behavior on ends.
	  Using cdna_direction information on single gaps.

2006-03-01 10:22  twu

	* src/stage3.c: Forcing single gaps to be solved.  Adding
	  cdna_direction information for single gaps.  Fixed problem with
	  short indels being inserted backward.

2006-03-01 10:21  twu

	* src/: oligoindex.c, oligoindex.h: Implemented new scheme for
	  detecting repetitive sequence on ends, based on changepoint
	  analysis

2006-03-01 10:20  twu

	* src/smooth.c: Fixed memory leak.

2006-03-01 10:20  twu

	* src/translation.c: Added check so we won't go beyond ends.
	  Assigned variables when npairs is too few.

2006-02-27 04:44  twu

	* src/: stage3.c, stage3.h: Minor bug fixes

2006-02-26 03:07  twu

	* src/: match.c, match.h, matchdef.h, matchpool.c, stage1.c:
	  Keeping track of number of pairings for each match, and placing a
	  limit on the number of matchpairs generated for each match with a
	  "promiscuous" variable

2006-02-24 22:01  twu

	* src/stage2.c: Made behavior similar for sequence and reverse
	  complement, including bug fix and using diffdistance rather than
	  querydistance

2006-02-24 04:39  twu

	* src/: pairpool.c, pairpool.h: Added procedure for counting result
	  of bounding operation

2006-02-24 04:38  twu

	* src/: pair.c, pair.h: Counting amino acids directly for protein
	  PSL output.  Fixed problem in coordinates output where chrstring
	  was NULL.

2006-02-24 04:38  twu

	* src/dynprog.c: Increased penalty for gaps in single alignments
	  and made them uniform across sequence quality

2006-02-24 04:37  twu

	* src/: smooth.c, smooth.h: Rewrite of code to use arrays instead
	  of lists.  Reduced definition of short exon.	Now deleting
	  consecutive strings of short exons.

2006-02-24 04:36  twu

	* src/translation.c: Noting large insertions and deletions of amino
	  acids, even if not a multiple of 3

2006-02-23 06:08  twu

	* src/: chimera.c, chimera.h, gmap.c, stage3def.h: Moved various
	  functions back to stage3.c

2006-02-23 06:08  twu

	* src/: stage3.c, stage3.h: Performing substitution of gaps only
	  for final cDNA direction

2006-02-23 06:07  twu

	* src/: oligoindex.c, oligoindex.h: Turned off trimming of sequence
	  for reference sequences and for protein sequences

2006-02-23 06:06  twu

	* src/: intron.c, intron.h: Using cdna_direction information in
	  assigning Intron_type

2006-02-23 06:06  twu

	* src/: dynprog.c, pairpool.c, pairpool.h, stage2.c: Passing in
	  gapp as a parameter to Pairpool_push

2006-02-23 06:03  twu

	* src/translation.c: Fixed bug with marking backwards cDNAs
	  relative to reference sequence

2006-02-22 11:04  twu

	* src/translation.c: Fixed minor bugs in new implementation

2006-02-22 09:55  twu

	* src/Makefile.am: Rewrite of code for determining mutations and
	  for printing the results.  Removed mutation.c and mutation.h.

2006-02-22 09:55  twu

	* src/: mutation.c, mutation.h, pair.c, pair.h, translation.c:
	  Rewrite of code for determining mutations and for printing the
	  results

2006-02-21 01:35  twu

	* src/stage3.c: Moved some chimera functions from stage3.c to
	  chimera.c.  Set acceptable_mismatches for microexons to be 2.

2006-02-21 01:35  twu

	* src/: Makefile.am, chimera.c, chimera.h, stage3.h, stage3def.h:
	  Moved some chimera functions from stage3.c to chimera.c

2006-02-21 01:33  twu

	* src/dynprog.c: Increased probability standard for finding
	  microexons

2006-02-19 11:59  twu

	* src/translation.c: Fixed bug where cDNA translation was
	  incomplete

2006-02-19 11:58  twu

	* src/stage3.c: Fixed bug in substitution for gaps when ngap is not
	  3

2006-02-19 11:20  twu

	* src/: stage3.c, stage3.h: Complete rewrite of stage 3 to use gap
	  pairs

2006-02-19 11:19  twu

	* src/translation.c: Increased parameter for ignoring amino acid
	  mismatches at ends of query sequence

2006-02-19 11:19  twu

	* src/: smooth.c, smooth.h: Made changes to handle new gap pairs

2006-02-19 11:18  twu

	* src/pair.c: No longer assigning coordinates for query sequence
	  and genomic segment within gaps

2006-02-19 11:17  twu

	* src/: matchpair.c, matchpair.h: Limiting 12-mer hits that are
	  considered in clustering method to those that have a neighboring
	  hit within the query length

2006-02-19 11:15  twu

	* src/: dynprog.c, dynprog.h: Inserting a single gap pair for
	  introns and cDNA insertions instead of filling in nucleotides

2006-02-19 11:14  twu

	* src/stage1.c: Reduced extension of genomic segment when cluster
	  mode is required

2006-02-19 11:13  twu

	* src/gmap.c: Put output to stderr when path not found in
	  compressed output

2006-02-19 11:12  twu

	* src/: intron.c, intron.h: Moved Intron_type function here

2006-02-19 11:11  twu

	* src/: pairpool.c, pairpool.h: Added explicit functios for
	  handling gap pairs

2006-02-19 11:11  twu

	* src/pairdef.h: Added fields for queryjump and genomejump, to be
	  used for gaps

2006-02-07 22:26  twu

	* src/translation.c: Set minimum number of pairs required for a
	  translation

2006-02-07 03:27  twu

	* src/gmap.c: Now checking for existence of -g or -d flag before
	  proceeding

2006-02-07 03:26  twu

	* src/stage3.c: Fixed problem when solving an intron and unable to
	  peel back anything.

2006-02-05 11:09  twu

	* src/dynprog.c: Fixed problem with extending 5' and 3' ends with
	  assumption of no gap.  Added extra efficiency based on this
	  assumption.

2006-01-19 07:08  twu

	* tests/: align.test.ok, map.test.ok: Changed "Mutations" to "Amino
	  acid changes" in output

2006-01-19 07:07  twu

	* README: Enhanced usage statement for gmap_setup

2006-01-19 07:06  twu

	* util/gmap_setup.pl.in: Cleaned up flags.  Added messages after
	  each make procedure.	Enhanced usage statement.

2006-01-19 06:33  twu

	* util/gmap_process.pl.in: Removed code for a separate strain file

2006-01-19 06:33  twu

	* util/gmap_process.pl.in: Added provision for a separate strain
	  file, but commented out code

2006-01-19 06:31  twu

	* util/md_coords.pl.in: Fixed problem when MD file has fewer than 6
	  lines.  Put output into an array for printing out in one batch.
	  Improved handling of strains.

2006-01-19 06:30  twu

	* util/fa_coords.pl.in: Put output into an array for printing out
	  in one batch.

2006-01-19 06:27  twu

	* util/: Makefile.am, pmap_setup.pl.in: Removed pmap_setup program

2006-01-19 06:27  twu

	* src/stage3.c: Added procedure to fix short gaps

2006-01-19 06:26  twu

	* src/gmapindex.c: Added ability to read reference strain from
	  coords file

2006-01-19 06:25  twu

	* src/gmap.c: Added provision for different stage 2 index size for
	  PMAP

2006-01-17 08:52  twu

	* src/pair.c: Fixed problem with protein PSL coordinates

2005-12-15 03:16  twu

	* src/: backtranslation.c, backtranslation.h: Fixed problems in
	  backtranslation when genomic segment has lower case characters

2005-12-15 03:15  twu

	* src/: gmap.c, stage3.c, stage3.h: Preserved diagnostic info in
	  PMAP through backtranslation

2005-12-15 03:14  twu

	* src/pair.c: Changed printing of cDNA on ambiguous comps to be
	  lower case if appropriate

2005-12-15 03:13  twu

	* src/dynprog.c: Changed ends from 1 gap to no gaps.  Changed
	  open/extend penalties at ends (which may be irrelevant now).

2005-12-14 22:24  twu

	* src/: matchpool.c, stage1.c: Fixed problems with genomic position
	  in reverse complement matches in PMAP.

2005-12-14 22:23  twu

	* src/translation.c: Fixed problems with ends of cDNA and genomic
	  translation for PMAP.  Set margin to zero for computing amino
	  acid changes.

2005-12-14 22:21  twu

	* src/iit-read.c: Commented out abort

2005-12-14 01:05  twu

	* src/sequence.c: Fixed uninitialized heap

2005-12-13 02:07  twu

	* src/: gmap.c, stage2.c, stage2.h: Added pruning before stage 2
	  based on number of potentially consecutive hits and short paths

2005-12-13 02:06  twu

	* src/: oligoindex.c, oligoindex.h: Added computation of
	  potentially consecutive hits in the query

2005-12-13 02:05  twu

	* src/stage1.c: Added filtering of matchlist based on support

2005-12-13 02:05  twu

	* src/: matchpair.c, matchpair.h: Added storage of support and usep
	  in Matchpair_T object

2005-12-09 00:57  twu

	* src/: stage2.c, gmap.c: Removed code for finding PMAP unaligned
	  access error

2005-12-09 00:56  twu

	* src/: stage2.c, gmap.c: Added code for finding PMAP unaligned
	  access error

2005-12-09 00:55  twu

	* src/: backtranslation.c, oligoindex.c: Removed code for checking
	  assertions

2005-12-09 00:54  twu

	* src/: backtranslation.c, oligoindex.c: Added code for checking
	  assertions

2005-12-08 04:43  twu

	* src/pair.c: Streamlined determination of amino acid coordinates
	  in alignment output

2005-12-08 04:42  twu

	* src/indexdb.c: Fixed bug in handling offsets in alternative
	  strains in PMAP

2005-12-08 04:41  twu

	* src/dynprog.c: Reformulated assignment of pointers in
	  two-dimensional array

2005-12-06 02:01  twu

	* src/translation.c: Formatting change

2005-12-06 02:00  twu

	* src/stage1.c: Turned on use of matchpool.  Fixed problem where
	  list was not reset to NULL.

2005-12-06 02:00  twu

	* src/pair.c: Changed dir:unknown to dir:indet

2005-12-06 01:59  twu

	* src/oligoindex.c: Fixed uninitialized variable in GMAP

2005-12-06 01:59  twu

	* src/matchpool.c: Improved debugging statements

2005-12-06 01:59  twu

	* src/matchpair.c: Increased standard for stage 1 support

2005-12-05 15:58  twu

	* src/oligoindex.c: Made code compatible with both GMAP and PMAP

2005-12-05 15:49  twu

	* src/: backtranslation.c, dynprog.c: Reduced memory allocation for
	  two-dimensional array into a one-dimensional array

2005-12-05 15:47  twu

	* src/: pairpool.c, matchpool.c: Removed initial creation of chunks

2005-12-05 15:47  twu

	* src/oligoindex.c: Fixed bug in PMAP where stop codon in the
	  genomic sequence created a value that exceeded oligospace

2005-12-05 10:17  twu

	* src/: pair.c, pair.h: Added a way for the thread worker id to be
	  printed with the result.  Removed ambiguous comp characters from
	  gmap.

2005-12-05 10:17  twu

	* src/: gmap.c, reqpost.c, reqpost.h, result.c, result.h, stage3.c,
	  stage3.h: Added a way for the thread worker id to be printed with
	  the result

2005-12-05 10:15  twu

	* src/matchpool.c: Added commands for saving and restoring
	  pointers, so memory can be re-used

2005-12-05 10:14  twu

	* src/: match.c, match.h, stage1.c: Added compiler conditions for
	  using matchpool method.

2005-12-05 10:12  twu

	* src/genome.c: Fixed messages to user

2005-12-05 08:55  twu

	* src/chrsubset.c: Changed format of output

2005-12-05 08:54  twu

	* src/translation.c: Fixed bug in translating backward cDNAs.
	  Extended translation all the way to the end.

2005-12-04 00:13  twu

	* src/: Makefile.am, gmap.c, matchpair.c, matchpair.h,
	  matchpairdef.h, matchpairpool.c, matchpairpool.h, stage1.c,
	  stage1.h: Removed special memory allocation routines for
	  matchpairs

2005-12-03 23:31  twu

	* src/: Makefile.am, gmap.c, match.c, match.h, matchpair.c,
	  matchpair.h, matchpairdef.h, matchpairpool.c, matchpool.c,
	  matchpool.h, stage1.c, stage1.h, matchpairpool.h: Added special
	  memory allocation routines for matches and matchpairs

2005-12-03 23:29  twu

	* src/iit-read.c: Added an exception handler

2005-12-03 23:29  twu

	* src/pair.c: Commented out unused procedure

2005-12-03 23:28  twu

	* src/genome.c: Added include of except.h

2005-12-02 07:00  twu

	* src/gmap.c: Fixed memory leak

2005-12-02 06:59  twu

	* src/translation.c: Added separate routine for printing list of
	  mutations.  Fixed problem where number of cDNA nucleotides in
	  codon is 4 or 5.

2005-12-02 06:58  twu

	* src/stage2.c: Clarified different code for gmap and pmap

2005-12-02 06:58  twu

	* src/stage1.c: Added checking routine for Stage1 object

2005-12-02 06:57  twu

	* src/sequence.c: Fixed case where first sequence of FASTA file has
	  no header, but subsequent sequences do.

2005-12-02 06:55  twu

	* src/nr-x.c: Initial import into CVS

2005-12-02 06:55  twu

	* src/pair.c: Added printing of aapos to all positions in "f -9"
	  mode

2005-12-02 06:55  twu

	* src/mutation.c: Simplified logic of merge functions

2005-12-02 06:54  twu

	* src/: mem.c, access.c: Augmented debugging statements

2005-11-29 01:33  twu

	* src/match.h: Provided interface for new functions

2005-11-29 01:32  twu

	* src/gmap.c: Fixed bug due to switched parameters

2005-11-29 01:25  twu

	* src/stage3.c: Added comment

2005-11-29 01:24  twu

	* config.site: Added information about defaults

2005-11-29 01:23  twu

	* README: Added information about Cygwin and defaults

2005-11-28 09:37  twu

	* src/stage1.c: Added include of match.h

2005-11-23 01:30  twu

	* config/fopen.m4, acinclude.m4, configure.ac: Added commands to
	  check for 'b' or 't' flag to fopen

2005-11-23 01:30  twu

	* src/pmap.c: Removed obsolete file

2005-11-23 01:29  twu

	* src/: Makefile.am, access.c, chrsubset.c, datadir.c, fopen.h,
	  genome-write.c, genomeplot.c, gmap.c, gmapindex.c, iit-read.c,
	  iit-write.c, iit_store.c, indexdb.c, oligo-count.c, pdldata.c,
	  pmapindex.c: All calls to fopen now generalized to handle systems
	  that allow or disallow the 'b' or 't' flag

2005-11-22 09:09  twu

	* VERSION: Updated version

2005-11-22 07:32  twu

	* tests/Makefile.am: Removed coords1.test, which is now performed
	  by setup1.test and setup2.test

2005-11-22 07:31  twu

	* tests/: setup1.test.in, setup2.test.in: Added prerequisite of
	  fa_coords program for setup tests

2005-11-22 07:31  twu

	* README: Made instructions for raw genome build match changes in
	  gmap_setup

2005-11-22 07:30  twu

	* util/gmap_setup.pl.in: Changed name of make command

2005-11-22 02:52  twu

	* util/gmap_setup.pl.in: Clarified comments

2005-11-22 02:52  twu

	* src/gmap.c: Made npaths output correct when user provides a
	  segment

2005-11-22 02:51  twu

	* src/: match.c, matchdef.h, stage1.c: Storing reciprocal of
	  nentries to avoid repeating this calculation multiple times later

2005-11-22 02:50  twu

	* tests/: setup1.test.in, setup2.test.in: Made changes in test to
	  match changes in program

2005-11-22 02:50  twu

	* tests/: align.test.ok, map.test.ok: Made change in output from
	  Mutations to Amino acid changes

2005-11-22 02:50  twu

	* tests/Makefile.am: Made change in name of coords file

2005-11-22 02:49  twu

	* README: Made instructions consistent with changes in programs

2005-11-21 11:58  twu

	* util/fa_coords.pl.in: Changed a flag.  Output now going to stdout
	  rather than stderr.

2005-11-21 11:57  twu

	* util/gmap_setup.pl.in: Now making the call to fa_coords or
	  md_coords within the Makefile

2005-11-21 10:40  twu

	* src/matchpair.c: Turned off debugging

2005-11-21 10:39  twu

	* src/: match.c, match.h, matchdef.h: Storing number of entries for
	  each match

2005-11-21 10:39  twu

	* src/indexdb.c: Moved one type of debug macro into its own
	  category

2005-11-21 10:38  twu

	* src/stage1.c: Weighted dangling computation according to number
	  of entries for each match

2005-11-21 10:37  twu

	* src/translation.c: Fixed bug where pointer went past beyond
	  sequence

2005-11-19 03:18  twu

	* src/: chrsubset.c, gmap.c: Added printing of chrsubset
	  information.	Consolidated printing of npaths information into a
	  single function.

2005-11-19 03:11  twu

	* src/backtranslation.c: Using the two aamarkers.  Allowing matches
	  to codons even for frameshifts.

2005-11-19 01:07  twu

	* src/mutation.c: Allowed merging of adjacent insertions

2005-11-19 00:23  twu

	* src/translation.c: Made PMAP assignment of genomic amino acids
	  conform to GMAP code for assignment of cDNA amino acids

2005-11-18 23:38  twu

	* src/translation.c: Added further translation of cDNA beyond
	  genomic stop codon, if possible

2005-11-18 23:29  twu

	* src/translation.c: Streamlined code for amino acids to cDNA
	  sequence

2005-11-18 17:27  twu

	* src/translation.c: Overhaul of method for assigning amino acids
	  to cDNA sequence, now based on separate marking and assignment of
	  codons.

2005-11-18 17:26  twu

	* src/: pair.c, pairdef.h, pairpool.c: Created separate aamarkers
	  for genomic and cDNA sequence

2005-11-18 14:36  twu

	* src/: gmap.c, params.c, params.h, stage3.c, stage3.h,
	  translation.c, translation.h: Added flag for specifying maximum
	  number of amino acid changes to show

2005-11-18 12:56  twu

	* src/stage1.c: Fixed memory leak

2005-11-18 12:56  twu

	* src/matchpair.c: Fixed read of uninitialized heap when bestsize
	  == 0

2005-11-18 12:25  twu

	* src/: matchpair.c, matchpair.h: Removed storage of support value

2005-11-18 12:22  twu

	* src/: gmap.c, matchpair.c, matchpair.h, stage1.c: Moved sequence
	  pruning procedures from gmap.c to matchpair.c

2005-11-18 08:40  twu

	* src/stage1.c: Fixed bug which caused loop to continue
	  unnecessarily

2005-11-18 07:25  twu

	* src/: gmap.c, result.c, stage1.h: Added complete option for
	  freeing Stage 1 objects

2005-11-18 07:24  twu

	* src/stage1.c: Introduced idea of stepping through trials to
	  identify poor genomic matches

2005-11-18 07:23  twu

	* src/: matchpair.c, matchpair.h: Introduced method for salvaging
	  individual 12-mer hits

2005-11-18 05:04  twu

	* src/: gmap.c, stage1.c, stage1.h: Simplified call to
	  Stage1_matchlist

2005-11-18 04:43  twu

	* src/stage1.c: Cleaning up parameters in preparation for cycling
	  through stage 1

2005-11-17 09:54  twu

	* src/indexdb.c: Added forward/backward to pre-loading messages for
	  pmap

2005-11-17 09:54  twu

	* src/translation.c: Skipping mutation calls on non-standard amino
	  acids

2005-11-17 09:53  twu

	* src/backtranslation.c: Fixed bug when trying to backtranslate
	  non-standard amino acids

2005-11-17 05:37  twu

	* util/gmap_setup.pl.in: Added intermediate commands to Makefile

2005-11-11 06:14  twu

	* src/backtranslation.c: Improved matching of genomic codon to cdna
	  codon.

2005-11-11 06:13  twu

	* src/translation.c: Added debugging statement

2005-11-11 06:13  twu

	* src/pair.c: Restored printing of genomic sequence for ambiguous
	  matches in pmap

2005-11-10 05:06  twu

	* src/genome-write.c: Added read of linefeed after FASTA entry in
	  raw genome files.  Improved speed of writing blocks of zeros or
	  X's.

2005-11-10 05:05  twu

	* src/gmapindex.c: Fixed bug in skip_sequence for raw genome files

2005-11-10 05:05  twu

	* src/get-genome.c: Implemented printing of raw genome files

2005-11-10 04:26  twu

	* src/: gmap.c, stage3.c, stage3.h: Moved final translation and
	  backtranslation steps into print procedures

2005-11-10 04:24  twu

	* src/: Makefile.am, backtranslation.c, backtranslation.h,
	  translation.c, translation.h: Moved nucleotide consistency
	  procedures for pmap into backtranslation.c

2005-11-10 04:21  twu

	* src/pair.c: Removed consistency conversion.  Now being done by
	  backtranslation procedures.  Removed meaning of AMBIGUOUS_COMP
	  for compressed output of pmap.

2005-11-10 01:38  twu

	* src/dynprog.c: Added actual coordinates to debugging statements

2005-11-10 01:36  twu

	* src/translation.h: Made backtranslation procedure more rigorous.

2005-11-10 01:36  twu

	* src/translation.c: Made backtranslation procedure more rigorous.
	  Added debugging statements.

2005-11-09 07:39  twu

	* src/get-genome.c: Changed -r flag to also indicate use of the
	  uncompressed genome file

2005-11-09 06:05  twu

	* src/: get-genome.c, sequence.c, sequence.h: Added uncompressed
	  raw format for printing genome segment

2005-11-09 06:04  twu

	* src/: genome-write.c, genome-write.h, gmapindex.c: Added
	  uncompressed raw format for genome file

2005-11-08 09:13  twu

	* src/pair.c: Reformulated printing of protein-based PSL output

2005-11-08 09:12  twu

	* src/intlist.c: Added include of stdio.h

2005-11-08 09:12  twu

	* src/chimera.c: Removed include of nmath.h

2005-11-08 09:11  twu

	* src/gmap.c: Allowed coordinate output for pmap.  Changed flag to
	  -f 9.

2005-11-04 08:31  twu

	* util/gmap_compress.pl.in: Allowed handling of PMAP output

2005-11-04 08:31  twu

	* util/gmap_uncompress.pl.in: Fixed bug in printing last line of
	  alignment

2005-11-01 08:37  twu

	* src/: gmap.c, pair.c, pair.h, stage3.c, stage3.h: Allowed introns
	  to be printed in exon mode

2005-11-01 08:37  twu

	* src/matchpair.c: Imposed the requirement that minsize be 2 or
	  more away from bestsize

2005-10-31 03:02  twu

	* src/: gmap.c, pair.c, pair.h, stage3.c, stage3.h: Added ability
	  to print exons using genomic sequence

2005-10-28 01:51  twu

	* src/indexdb.c: Using lseek instead of fseek/fseeko for writing a
	  positions file on disk

2005-10-28 01:50  twu

	* src/: access.c, access.h: Added a function for opening a file as
	  read/write

2005-10-27 08:56  twu

	* VERSION: Updated version

2005-10-27 08:56  twu

	* tests/Makefile.am: Restored setup2.test

2005-10-27 08:55  twu

	* tests/setup2.test.in: Made test use new gmap_setup script

2005-10-27 08:55  twu

	* tests/setup1.test.in: Removed install step

2005-10-27 08:55  twu

	* util/gmap_setup.pl.in: Fixed bug in clean statement

2005-10-27 08:54  twu

	* configure.ac: Added check for fseeko

2005-10-27 08:53  twu

	* src/gmap.c: Added information about various type sizes to -V flag

2005-10-27 08:52  twu

	* src/: indexdb.c, genome-write.c, compress.c: Using fseeko if
	  available

2005-10-25 14:11  twu

	* util/gmap_setup.pl.in: Fixed bug where -W flag was in the wrong
	  branch

2005-10-25 04:03  twu

	* src/pair.c: Removed extraneous linefeed in compressed output

2005-10-25 04:00  twu

	* VERSION: Updated version number

2005-10-25 03:58  twu

	* src/pair.c: Fixed psl output

2005-10-25 03:58  twu

	* README: Clarified use of ./configure flags.  Added instructions
	  for the -C flag in fa_coords.

2005-10-25 03:07  twu

	* util/gmap_setup.pl.in: Restored -W flag for writing directly to
	  file

2005-10-25 02:52  twu

	* util/gmap_setup.pl.in: Added instructions for clean to Makefile

2005-10-25 02:52  twu

	* util/fa_coords.pl.in: Added -C flag to make each sequence a
	  separate chromosome

2005-10-25 02:50  twu

	* src/: pair.c, pair.h, stage3.c: Added printing of cDNA direction
	  in compressed output

2005-10-25 02:49  twu

	* src/: bigendian.h, mem.h: Added include of config.h.

2005-10-21 03:37  twu

	* VERSION: Updated version

2005-10-21 02:56  twu

	* README: Added instructions for running make after gmap_setup

2005-10-21 02:55  twu

	* MAINTAINER: Added reminder to check for DEBUG mode

2005-10-21 02:51  twu

	* src/pdldata.c: Fixed typo

2005-10-21 02:50  twu

	* src/: pair.c, pair.h, stage3.c, stage3.h: Restored printing of
	  strain information

2005-10-21 02:50  twu

	* src/oligo-count.c: Using new interface to indexdb

2005-10-21 02:49  twu

	* src/gmap.c: Added error message if user tries to use strain
	  information and file is not found

2005-10-21 02:43  twu

	* src/gmap.c: Restored printing of strain information.	Added
	  conversion to upper case for altstrain sequence.

2005-10-21 02:42  twu

	* src/: genome.c, indexdb.c: Added printing of number of bytes

2005-10-21 02:42  twu

	* src/access.h: Added MAX32BIT

2005-10-21 02:42  twu

	* src/access.c: Added debugging statements

2005-10-21 02:40  twu

	* src/Makefile.am: Added needed files

2005-10-18 14:11  twu

	* configure.ac: Added warning message if mmap not available

2005-10-18 14:11  twu

	* util/fa_coords.pl.in: Added ability to read from stdin

2005-10-18 14:10  twu

	* tests/setup1.test.in: Added install command

2005-10-18 14:10  twu

	* src/: access.c, access.h: Made Access_filesize an external
	  routine

2005-10-18 14:09  twu

	* src/: genuncompress.c, pdldata.c: Using routines from access.c

2005-10-18 13:57  twu

	* src/Makefile.am: Added access.c and access.h to programs with
	  IIT_T object

2005-10-18 13:56  twu

	* src/chrsubset.c: Added include of config.h

2005-10-18 13:55  twu

	* src/gmapindex.c: Removing free of accsegmentpos_table, which
	  fails on some computers

2005-10-18 13:54  twu

	* src/gmap.c: Reading user-provided genomic segment and reference
	  sequence before FASTA query

2005-10-18 13:53  twu

	* src/: genome-write.c, genomeplot.c, get-genome.c, iit_dump.c,
	  iit_get.c, pmapindex.c, segmentpos.c: Changed calls to IIT_free
	  and IIT_annotation

2005-10-18 13:51  twu

	* src/: iit-write.c, iit-write.h: Made write version of IIT_free
	  static and renamed it.

2005-10-18 13:50  twu

	* src/iit-read.h: Changed interface to IIT_annotation.

2005-10-18 13:50  twu

	* src/iit-read.c: Added FILEIO mode for reading IIT_T objects.
	  Changed interface to IIT_annotation.

2005-10-18 13:48  twu

	* src/iitdef.h: Made mutex part of IIT_T object.  Added offset to
	  IIT_T object for FILEIO mode.

2005-10-18 13:47  twu

	* src/indexdb.c: Made mutexes part of Indexdb_T object.  Changed
	  calls to IIT_annotation.

2005-10-18 13:43  twu

	* src/genome.c: Made mutex part of Genome_T object

2005-10-18 13:42  twu

	* src/access.h: Added flag for randomp.  Added function for
	  read/write mmap.

2005-10-18 13:41  twu

	* src/access.c: Moved file size determination to a separate
	  function

2005-10-14 06:25  twu

	* src/gmap.c: Moved reading of input sequences to beginning

2005-10-14 06:25  twu

	* src/indexdb.c: Minor fixes

2005-10-14 06:24  twu

	* src/access.h: Returning length and time for Access_immediate

2005-10-14 06:24  twu

	* src/access.c: Returning length and time for Access_immediate.
	  Forcing read of pages during pre-load.

2005-10-14 05:36  twu

	* src/gmap.c: Removed unused variables

2005-10-14 05:35  twu

	* src/result.c: Addressed compiler warning

2005-10-14 05:35  twu

	* src/pair.c: Fixed faulty print statement in pslformat_nt

2005-10-14 05:35  twu

	* src/indexdb.c: Added necessary include file.	Removed unnecessary
	  variables.

2005-10-14 05:34  twu

	* src/: genome.c, stage3.c: Added necessary include file

2005-10-14 05:34  twu

	* src/dynprog.c: Applied type conversion for char to access array

2005-10-14 05:33  twu

	* src/datadir.c: Removed unused variables

2005-10-14 05:06  twu

	* src/Makefile.am: Added access.c and access.h

2005-10-14 05:05  twu

	* src/: blackboard.c, blackboard.h, gmap.c: Added nextchar to
	  Blackboard_T object

2005-10-14 05:05  twu

	* src/gmap.c: Now reading first sequence in main thread, and using
	  existence of a second sequence to determine whether to start
	  threads and to pre-read offsets file for GMAP.  Conditioning some
	  flags based on existence of mmap and threading support.

2005-10-14 05:03  twu

	* src/datadir.h: Removed unnecessary include

2005-10-14 05:03  twu

	* src/intlist.c: Minor fix to resolve gcc compiler warning

2005-10-14 05:02  twu

	* src/: access.c, access.h, genome.c, indexdb.c: Standardized file
	  access routines and moved them to access.c

2005-10-13 13:36  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Fixed ASCII printing
	  of universal coordinates when a range is selected

2005-10-13 13:36  twu

	* src/matchpair.c: Fixed calculation of genome length for segment

2005-10-13 13:35  twu

	* src/sequence.c: Fixed Sequence_read_unlimited to handle sequences
	  without a header line.

2005-10-12 08:51  twu

	* util/gmap_setup.pl.in: Changed program to generate a Makefile

2005-10-12 08:50  twu

	* util/: fa_coords.pl.in, md_coords.pl.in: Deleted comment about
	  gmap_setup running time

2005-10-12 08:50  twu

	* util/gmap_process.pl.in: Initial import into CVS

2005-10-12 08:49  twu

	* util/Makefile.am: Added instructions for gmap_process

2005-10-12 08:49  twu

	* tests/setup1.test.in: Modified setup test for new interface to
	  utility programs

2005-10-12 08:48  twu

	* tests/Makefile.am: Modified setup test to put binary files in
	  tests directory

2005-10-12 08:31  twu

	* MAINTAINER: Minor note to self

2005-10-12 04:02  twu

	* src/Makefile.am: Made FULLDIST work for gmap sources

2005-10-12 04:01  twu

	* src/gmap.c: Made separate flags for batch for offsets and batch
	  for positions file.  Simplified input thread.

2005-10-12 04:00  twu

	* src/indexdb.h: Made separate flags for batch for offsets and
	  batch for positions file

2005-10-12 04:00  twu

	* src/indexdb.c: Added memory mapping for offsets files under PMAP.
	  Made separate flags for batch for offsets and batch for
	  positions file.

2005-10-12 03:59  twu

	* src/oligoindex.c: Removed stop codon from oligomers in stage 2

2005-10-12 02:25  twu

	* src/Makefile.am: Moved beta code for GMAP into a separate program

2005-10-12 02:25  twu

	* src/stage2.c: Moved PMAP conditionals out of debugging statements

2005-10-11 08:10  twu

	* src/Makefile.am: Removed conditional distribution of files

2005-10-11 08:10  twu

	* src/translation.c: Including comp.h header

2005-10-11 08:10  twu

	* src/oligop.c: Removed STOP from amino acid alphabet.

2005-10-11 08:09  twu

	* src/gmapindex.c: Generating chrsubset file at same time as
	  chromosome file

2005-10-11 08:09  twu

	* src/: gmap.c, pmapindex.c: Changed PMAP indexing interval to be
	  based on amino acids.

2005-10-11 08:08  twu

	* src/indexdb.h: Removed STOP from amino acid alphabet.  Changed
	  PMAP interval to be based on amino acids.

2005-10-11 08:08  twu

	* src/indexdb.c: Simplified conversion of oligomer to amino acid
	  index for PMAP.  Removed STOP from amino acid alphabet.
	  Computing each protein frame separately.

2005-10-11 03:38  twu

	* configure.ac: Added large file support with AC_SYS_LARGEFILE.
	  Removed setup test number 2.	Added gmap_process.

2005-10-11 03:37  twu

	* acinclude.m4: Removed macros for O_LARGEFILE

2005-10-11 03:35  twu

	* config/open-flags.m4: Removed file open-flags.m4

2005-10-10 02:30  twu

	* config/open-flags.m4, acinclude.m4: Added check for O_LARGEFILE
	  in open

2005-10-07 01:19  twu

	* util/gmap_setup.pl.in: Restored -W flag and improved it

2005-10-06 09:17  twu

	* VERSION: Updated version

2005-10-06 09:17  twu

	* configure.ac: Added hook for pmap_setup.pl

2005-10-06 09:16  twu

	* README: Added explanation of full, uncompressed genome, and of
	  batch modes

2005-10-06 09:16  twu

	* util/gmap_setup.pl.in: Added checks to make sure desired files
	  are built.  Added printing of commands to stdout.

2005-10-06 09:15  twu

	* util/pmap_setup.pl.in: Added checks to make sure desired files
	  are built

2005-10-06 09:15  twu

	* util/: gmap_compress.pl.in, gmap_uncompress.pl.in: Altered format
	  of compressed output to indicate ambiguous matches

2005-10-06 08:55  twu

	* src/pair.c: Altered format of compressed output to indicate
	  ambiguous matches

2005-10-06 08:54  twu

	* src/genome.c: Fixed batch loading of full genomes greater than 2
	  gigabytes

2005-10-06 06:44  twu

	* src/gmap.c: Modified message about batch mode and multiple
	  threads mode

2005-10-06 06:43  twu

	* src/stage2.c: Parameterized alignment characters and defined them
	  centrally in comp.h.	Restored previous intron penalties based on
	  length.

2005-10-06 06:43  twu

	* src/pair.c: Parameterized alignment characters and defined them
	  centrally in comp.h.	Now printing ambiguous nucleotide matches.

2005-10-06 06:42  twu

	* src/dynprog.c: Parameterized alignment characters and defined
	  them centrally in comp.h.  Added separate table for consistent
	  nucleotide pairs.

2005-10-06 06:42  twu

	* src/: Makefile.am, comp.h, pairpool.c, stage3.c, translation.c:
	  Parameterized alignment characters and defined them centrally in
	  comp.h

2005-10-05 10:01  twu

	* src/gmap.c: Changed batch mode to be of two types: pre-loading of
	  indices only, and pre-loading of both indices and genome.

2005-10-05 07:05  twu

	* src/gmap.c: Clarified various user messages

2005-10-05 07:01  twu

	* src/indexdb.c: Added an explicit check for a nonsensical offsets
	  file

2005-10-05 07:01  twu

	* src/pair.c: Made margin width determined dynamically in printing
	  the alignments

2005-10-03 10:16  twu

	* src/dynprog.c: Removed reverse intron possibilities from PMAP

2005-10-03 10:16  twu

	* src/gmapindex.c: Restored monitoring output for logging contigs

2005-10-03 10:15  twu

	* src/indexdb.c: Added fwd/rev to monitoring commands for indexing
	  offsets and position files

2005-10-03 10:15  twu

	* src/compress.c: Added monitoring commands for compressing and
	  uncompressing files

2005-10-03 10:12  twu

	* util/gmap_setup.pl.in: Clarified behavior and instructions for
	  building a full (uncompressed) genome file

2005-10-03 10:11  twu

	* util/fa_coords.pl.in: Abbreviated monitoring output, with a
	  parameter that controls which contigs to ignore

2005-10-03 10:10  twu

	* util/Makefile.am: Added make instructions for pmap_setup

2005-10-03 10:09  twu

	* util/pmap_setup.pl.in: Initial import into CVS

2005-10-01 01:34  twu

	* src/gmap.c: Performing translation of query sequence and genomic
	  segment to upper case.  Turned off stage 1 for user-provided
	  genomic segment in PMAP.  Provided -G flag for specifying full
	  genome, if it exists.

2005-10-01 01:32  twu

	* src/genome.c: Turned warning into error, if user wishes to use a
	  full genome and none exists

2005-10-01 01:31  twu

	* src/dynprog.c: Allowed intron gap parameter to be arbitrarily
	  large

2005-10-01 01:31  twu

	* src/: pair.c, stage2.c, translation.c: Fixed handling of
	  user-provided genomic segment with lower case characters for PMAP

2005-10-01 01:30  twu

	* src/stage1.c: Improved debugging statement

2005-10-01 01:30  twu

	* src/oligoindex.c: Minor formatting change

2005-10-01 01:29  twu

	* src/mem.c: Enhanced trap features

2005-10-01 01:29  twu

	* src/boyer-moore.c: Removed assertions

2005-09-30 15:35  twu

	* src/: boyer-moore.c, dynprog.c, dynprog.h, stage3.c, stage3.h:
	  Made stage 3 use upper case for query sequence and genomic
	  segment when needed, but original sequences for building
	  alignment

2005-09-30 15:13  twu

	* src/: oligoindex.c, oligoindex.h, stage2.c, stage2.h: Made stage
	  2 use upper case for query sequence and genomic segment for
	  oligomer chaining, but original sequences for building alignment

2005-09-30 15:06  twu

	* src/: oligo.c, oligop.c, stage1.c, stage1.h: Made stage 1 assume
	  upper case query sequence

2005-09-30 15:04  twu

	* src/pair.c: Removed call to toupper

2005-09-30 15:03  twu

	* src/: complement.h, sequence.c, sequence.h: Provided utilities
	  for making uppercase and alias versions of sequences

2005-09-30 15:02  twu

	* src/compress.c: Added toupper as reason for including ctype.h

2005-09-30 06:43  twu

	* src/plotdata.c: Revised autoscale function

2005-09-29 10:23  twu

	* src/stage2.c: For PMAP, fixed bug where C terminus of query
	  sequence was not aligned.  Eliminated computation of reverse
	  intron direction for PMAP.

2005-09-29 10:21  twu

	* src/oligoindex.c: Modified comments

2005-09-29 10:21  twu

	* src/gmap.c: Removed Sequence_trim for PMAP, and reduced stage 2
	  indexsize.

2005-09-29 10:20  twu

	* src/pair.c: Changed psl output to reflect definition of a block
	  to be a region without indels or gaps, instead of an exon

2005-09-21 23:39  twu

	* src/oligoindex.c: Make amino acid index for stage 2 (with 21
	  amino acids) distinct from that of stage 1 (with 16)

2005-09-21 23:37  twu

	* src/: indexdb.c, indexdb.h, oligop.c: Compressing 21 amino acids
	  into 16 to allow offsets of amino acid 7-mers to fit into less
	  than 2 GB

2005-09-21 08:39  twu

	* src/stage1.c: Parameterized size of oligomers for PMAP

2005-09-21 08:38  twu

	* src/: gmap.c, indexdb.h: Parameterized interval for stage 1 when
	  user provides a genomic segment

2005-09-21 08:35  twu

	* src/pmapindex.c: Parameterized size of oligomers

2005-09-21 08:35  twu

	* src/matchpair.c: Turned off debugging

2005-09-21 08:34  twu

	* src/: indexdb.h, indexdb.c: Introduced indexing of 7-mers by PMAP

2005-09-21 02:13  twu

	* VERSION: Updated version

2005-09-21 02:12  twu

	* util/gmap_setup.pl.in: Commented out -W flag for forcing write to
	  file.  Added option -G for making an uncompressed version of the
	  genome (.genome file).

2005-09-21 02:10  twu

	* util/fa_coords.pl.in: Allowed both chr and Chr in parsing for
	  chromosomal mapping

2005-09-21 02:09  twu

	* config.site: Clarified possible choices for LDFLAGS

2005-09-21 02:08  twu

	* src/matchpair.c: Penalizing clusters spread out in repetitive
	  genomic regions

2005-09-21 02:08  twu

	* src/pdlimage.c: Made images in color

2005-09-20 11:42  twu

	* src/gmapindex.c: Commented out monitoring statement about logging
	  contigs

2005-09-20 11:40  twu

	* src/stage1.c: Fixed a bug involving subtraction of two unsigned
	  ints into a signed int, occurring for chromosomes greater than
	  2^31 in length.

2005-09-19 05:00  twu

	* src/stage2.c: Fixed bug when stage 2 fails

2005-09-19 04:59  twu

	* src/pair.c: Fixed assessment of unknown bases for PMAP queries

2005-09-19 04:59  twu

	* src/matchpair.c: Fixed computation of stretch for PMAP protein
	  queries

2005-09-19 04:58  twu

	* src/indexdb.c: Removed debugging flag

2005-09-19 04:58  twu

	* src/iit_get.c: Added termination message and flushing output when
	  input coming from stdin

2005-09-19 04:57  twu

	* src/gmap.c: Added debugging messages

2005-09-16 02:50  twu

	* src/: Makefile.am, pdlimage.c: Initial addition of pdlimage to
	  CVS.

2005-09-08 03:49  twu

	* src/: intlist.c, intlist.h: Added command for Intlist_to_string

2005-09-08 03:49  twu

	* src/: iit-read.c, iit-read.h, stage3.c: Added option to print
	  levels of map results

2005-09-08 03:48  twu

	* src/gmap.c: Modified directory printing to go to a given file
	  pointer.  Added information about default directory to
	  print_version command.

2005-09-08 03:48  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Changed format of
	  positions file.  Changed title for summary genome plots.

2005-09-08 03:46  twu

	* src/: datadir.c, datadir.h, get-genome.c: Modified directory
	  printing to go to a given file pointer

2005-09-06 10:37  twu

	* src/get-genome.c: Added ability to print levels of map contents.
	  Fixed bug in interpreting an entire chromosome.

2005-09-02 11:18  twu

	* src/: genomeplot.c, pdldata.c, pdldata.h, plotdata.c, plotdata.h:
	  Generalized variable for transform and added reciprocal

2005-09-02 10:56  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Added option to
	  autoscale

2005-09-02 10:43  twu

	* src/: genomeplot.c, pdldata.c, pdldata.h, plotdata.c, plotdata.h:
	  Added options for computing summary of multiple samples

2005-09-02 07:55  twu

	* src/: plotdata.c, plotdata.h, genomeplot.c: Added functions for
	  printing a threshold line, and for printing output in ascii
	  format.

2005-09-02 07:54  twu

	* src/pdldata.c: Now removing line feeds from annotations.  If no
	  annotations are available, using sample numbers.

2005-08-29 06:23  twu

	* src/: plotgenes.c, plotgenes.h: Improved display of genes

2005-08-29 06:23  twu

	* src/genomeplot.c: Made changes so PDL file is read only when
	  necessary.  Added extra room for showing genes.

2005-08-26 06:41  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Printing accession
	  header only if one sample per page.  Reduced default number of
	  genomes per page to 12.

2005-08-26 05:43  twu

	* src/: genomeplot.c, pdldata.c, pdldata.h, plotdata.c: Added
	  ability to read sample identifiers from a separate file for PDL
	  input

2005-08-26 03:01  twu

	* src/genomeplot.c: Added ability to plot a single page

2005-08-23 10:22  twu

	* src/: gmap.c, pair.c, pair.h, stage3.c, stage3.h: For PMAP,
	  allowed PSL output in both nucleotide coordinates and protein
	  coordinates

2005-08-23 08:24  twu

	* src/: genomeplot.c, plotgenes.c, plotgenes.h, Makefile.am: Added
	  ability to plot genes

2005-08-18 09:59  twu

	* src/: plotdata.c, plotdata.h: Added options for printing dots and
	  overlapping samples

2005-08-18 09:59  twu

	* src/: pair.c, pair.h: Added option for printing coordinates.
	  Trying to fix PSL output for PMAP.

2005-08-18 09:58  twu

	* src/: gmap.c, stage3.c, stage3.h: Added option for printing
	  coordinates

2005-08-18 09:58  twu

	* src/genomeplot.c: Added option for printing dots and overlapping
	  samples

2005-08-18 09:57  twu

	* src/: color.c, color.h: Added color brewer palette

2005-08-18 06:46  twu

	* src/plotdata.c: Prevented printing of empty strings

2005-08-16 00:30  twu

	* src/: plotdata.c, plotdata.h: Fixed bug when only a subset of
	  genes is selected.  Added commands for gif output.

2005-08-16 00:28  twu

	* src/: get-genome.c, gmap.c: Showing available map files when
	  valid one is not entered

2005-08-16 00:28  twu

	* src/: datadir.c, datadir.h: Added function to list directory
	  contents

2005-08-16 00:27  twu

	* src/genomeplot.c: Allowed user to specify a list of samples to
	  plot

2005-08-16 00:26  twu

	* src/: intlist.c, intlist.h: Added function Intlist_from_string

2005-08-16 00:26  twu

	* src/stage3.c: Fixed mapping to account for cDNA direction

2005-08-10 08:35  twu

	* src/: Makefile.am, genomeplot.c, pdldata.c, pdldata.h,
	  plotdata.c, plotdata.h: Allowed genomeplot to read PDL files

2005-08-06 23:39  twu

	* src/iit-read.c: Improved debugging statements

2005-08-06 23:38  twu

	* src/: gmap.c, stage3.c, stage3.h: Added option to map by exons

2005-08-06 23:38  twu

	* src/: pair.c, pair.h: Added function to retrieve exon bounds

2005-08-04 00:51  twu

	* src/gmap.c: Merged pmap main code into gmap.c

2005-08-04 00:51  twu

	* src/: sequence.c, sequence.h: Added functionality for pmap
	  chimeras

2005-08-04 00:50  twu

	* src/: stage3.c, stage3.h: Changed function to take queryntlength
	  instead of queryseq.	Made function work with both gmap and pmap.

2005-08-04 00:49  twu

	* src/: chimera.c, chimera.h: Changed functions to take
	  queryntlength instead of queryseq

2005-08-04 00:47  twu

	* src/Makefile.am: Merged pmap main code into gmap.c

2005-08-04 00:03  twu

	* src/pair.c: Made PSL format for proteins print protein
	  coordinates

2005-08-03 12:31  twu

	* src/: chimera.c, chimera.h, gmap.c: Changed chimera algorithm to
	  potentially search both sides of an incomplete alignment

2005-08-02 02:45  twu

	* src/stage3.c: Increased size of merge length for chimeric
	  exon-exon junctions

2005-08-02 02:45  twu

	* src/sequence.c: Restored trimming of subsequences

2005-08-01 07:11  twu

	* src/: stage3.c, stage3.h: Changed chimeric margin detection to
	  work on both ends

2005-08-01 07:10  twu

	* src/stage1.c: Added debugging statements

2005-08-01 07:10  twu

	* src/: chimera.c, chimera.h, gmap.c: Changed chimeric search to
	  work on both ends that fail to align

2005-08-01 07:09  twu

	* src/sequence.c: Turned trimming off for subsequences

2005-08-01 07:09  twu

	* src/: pair.c, pair.h: Added indel penalties at appropriate end
	  for chimeric path scores

2005-07-31 23:29  twu

	* src/chimera.c: Tested code for checking if breakpoint is outside
	  the alignment

2005-07-31 23:28  twu

	* src/: get-genome.c, Makefile.am: Allowed user to look up
	  information in map iit files

2005-07-29 05:53  twu

	* src/: datum.c, datum.h, genomeplot.c, plotdata.c, plotdata.h:
	  Allowed colors to be specified in input file

2005-07-29 04:05  twu

	* src/: plotdata.c, genomeplot.c, chrsubset.c, chrsubset.h:
	  Implemented user-selected genomic range

2005-07-28 03:04  twu

	* src/plotdata.c: Allowed program to handle NaNQs

2005-07-28 02:46  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Added log and signed
	  cube root functions

2005-07-27 22:05  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Added ability to
	  print genome on a single line

2005-07-27 09:49  twu

	* src/genomeplot.c: Added ability to handle multiple samples

2005-07-27 09:49  twu

	* src/: plotdata.c, plotdata.h: Added ability to detect and read
	  header lines.  Made code for starting and ending pages extern.

2005-07-27 08:30  twu

	* src/: plotdata.c, plotdata.h, genomeplot.c: Implemented printing
	  of circular genome

2005-07-26 14:17  twu

	* src/pair.c: Corrected query coordinates of chimera in compressed
	  mode

2005-07-26 14:14  twu

	* src/pairpool.c: Fixed problem where a gap was left at the 5' end
	  of a bounded transfer.

2005-07-26 06:41  twu

	* src/: datum.c, datum.h, genomeplot.c, plotdata.c, plotdata.h:
	  Added ability to read specified colors for each line

2005-07-26 05:52  twu

	* src/: datum.c, datum.h, genomeplot.c, plotdata.c, plotdata.h:
	  Allowed printing of segments between chromosomes

2005-07-25 04:00  twu

	* src/: pmap.c, stage3.c, stage3.h: Allowed chimeric pieces to be
	  merged over longer length if ends have strong splice sites

2005-07-25 03:59  twu

	* src/stage1.c: Restored reader overlap for longer sequences

2005-07-25 03:59  twu

	* src/: gmap.c, iit-read.c, iit-read.h: Added chromosomal positions
	  to map information

2005-07-25 03:58  twu

	* src/: chrnum.c, chrnum.h: Added function to get offset for a
	  chrnum

2005-07-25 03:57  twu

	* src/Makefile.am: Added chrsegment.h to sources for genomeplot

2005-07-22 15:03  twu

	* src/: gmap.c, pmap.c, stage3.c, stage3.h: Allowed two parts of
	  chimera to merge if close on the genome

2005-07-21 08:51  twu

	* src/: stage3.c, stage3.h, translation.c, translation.h: Clarified
	  code specific to PMAP and GMAP

2005-07-21 08:50  twu

	* src/sequence.c: Changed sequence header for PMAP to refer to
	  amino acids

2005-07-21 08:50  twu

	* src/: pair.c, pair.h: Added ability to print inferred nucleotide
	  sequence for PMAP

2005-07-21 08:50  twu

	* src/oligop.c: Clarified meaning of INDEX1PART to be number of
	  amino acids

2005-07-21 08:49  twu

	* src/pmapindex.c: Clarified meaning of INDEX1PART to be number of
	  nucleotides

2005-07-21 08:49  twu

	* src/oligo-count.c: Using new interface for Reader_new

2005-07-21 08:48  twu

	* src/: indexdb.c, indexdb.h: Clarified meaning of INDEX1PART to be
	  number of nucleotides for PMAP.

2005-07-21 08:48  twu

	* src/pmap.c: Removed -q flag for specifying stage 1 interval, and
	  removed -T flag for truncating sequence at full-length protein.
	  Specified -Q flag to be printing of inferred nucleotide sequence.

2005-07-21 08:46  twu

	* src/gmap.c: Removed -q flag

2005-07-21 08:46  twu

	* src/Makefile.am: Added beta source files for pmap

2005-07-21 08:45  twu

	* src/stage1.c: Introduced min intron length.  Clarified meaning of
	  INDEX1PART to be number of amino acids.  Added debugging
	  statements.

2005-07-21 08:44  twu

	* src/: reader.c, reader.h: Allowed crossover of start pointer and
	  end pointer so that middle oligomers will be read.  Should help
	  in mapping of short sequences.

2005-07-21 03:08  twu

	* src/: translation.c, translation.h: Moved combinatorial testing
	  of codons to translation step

2005-07-21 03:07  twu

	* src/stage3.h: Performing protein translation only when necessary.

2005-07-21 03:07  twu

	* src/stage3.c: Considering only forward intron directions for
	  pmap.  Performing protein translation only when necessary.

2005-07-21 03:06  twu

	* src/stage2.c: Considering only forward intron directions for pmap

2005-07-21 03:05  twu

	* src/sequence.c: Changed header line for pmap

2005-07-21 03:05  twu

	* src/pair.c: Made further changes to accommodate plus sign in
	  alignment

2005-07-21 02:59  twu

	* src/pair.c: Introduced plus sign in alignment

2005-07-21 02:59  twu

	* src/oligoindex.c: Improved efficiency of analyzing genomic
	  segment, by storing indices for each frame

2005-07-21 02:56  twu

	* src/genome.c: Added debugging statements

2005-07-21 02:55  twu

	* src/: dynprog.c, dynprog.h: Changed combinatorial instantiation
	  of codons to a single instantiation

2005-07-21 02:54  twu

	* src/: Makefile.am, params.c, params.h, pmap.c: Gave pmap the same
	  overall behavior as gmap, including multi-threading and flag
	  options

2005-07-19 03:54  twu

	* src/: Makefile.am, block.c, block.h, dynprog.c, dynprog.h,
	  gmap.c, indexdb.c, indexdb.h, oligoindex.c, oligop.c, oligop.h,
	  pair.c, pmap.c, pmapindex.c, sequence.c, sequence.h, stage1.c,
	  stage1.h, stage2.c, stage2.h, stage3.c, stage3.h, translation.c,
	  translation.h: Introduced pmap and pmapindex

2005-07-15 06:54  twu

	* src/get-genome.c: Added range format to allow negative lengths

2005-07-15 06:54  twu

	* src/genome.c: Added exception when requested length exceeds
	  allocated buffer length

2005-07-15 06:53  twu

	* src/except.c: Added printing of exception message

2005-07-15 06:53  twu

	* src/chimera.c: Fixed problem when donor or acceptor length
	  exceeded allocated buffer length

2005-07-15 06:52  twu

	* src/Makefile.am: Fixed handling of non-distributed source code

2005-07-15 06:51  twu

	* tests/align.test.ok: Changed genomic coordinate to match new
	  computation of coordinates in gaps

2005-07-15 06:51  twu

	* VERSION: Updated version number

2005-07-13 05:26  twu

	* src/dynprog.c: Made genomic positions on left and right ends of
	  gap constant, to avoid problems in stage 3 computations

2005-07-13 05:26  twu

	* src/memchk.c: Made procedures thread-safe

2005-07-13 05:26  twu

	* src/: stage3.c, stage3.h: Fixed genomic positions on left and
	  right ends of gap.  Removing gaps at 5' end, possibly introduced
	  by smoothing.

2005-07-13 05:25  twu

	* src/: mem.c, mem.h: Improved memory trap procedures

2005-07-13 05:24  twu

	* src/matchpair.c: Added check before freeing some possibly null
	  structures

2005-07-13 05:24  twu

	* src/genome.c: Removed duplicate FREE of filename

2005-07-13 05:24  twu

	* src/gmap.c: Fixed genomic positions on left and right ends of
	  gap.	Fixed bug when chimera was not reset to NULL.

2005-07-13 05:23  twu

	* src/: pair.c, pair.h: Fixed genomic positions on left and right
	  ends of gap

2005-07-12 04:02  twu

	* src/stage3.c: Fixed bugs in computing dual introns, dealing with
	  previously computed gaps, and returning coordinates for empty
	  peelbacks.

2005-07-12 04:01  twu

	* src/stage1.c: Increased parameters for maximum number of matching
	  pairs considered

2005-07-12 02:35  twu

	* src/pairpool.c: Enhanced debugging output

2005-07-12 02:35  twu

	* src/: pair.c, pair.h: Added procedure for printing a single pair

2005-07-12 02:35  twu

	* src/mutation.c: Changed unnamed unions to named unions

2005-07-08 08:48  twu

	* src/stage3.c: Added extra check to make sure pairs is non-empty

2005-07-08 08:47  twu

	* src/gmap.c: Initialized chimera to be NULL

2005-07-08 08:46  twu

	* src/oligoindex.c: Fixed bug caused by writing to a random
	  location when indexsize < 8.

2005-07-08 08:45  twu

	* src/mem.c: Improved trap code

2005-07-08 08:42  twu

	* src/memchk.c: Changed types to be consistent with regular version
	  of memory manager

2005-07-08 05:52  twu

	* src/memchk.c: Added checking implementation of memory manager

2005-07-08 05:20  twu

	* src/stage3.c: Fixed a segmentation fault bug.

2005-07-08 05:19  twu

	* src/stage2.c: Changed distpenalty to ignore query distance and
	  max_intronlength, and simplified computation.  These values were
	  probably not affecting previous computation anyway.

2005-07-08 05:17  twu

	* src/mutation.c: Fixed problem caused by removal of unnamed union

2005-07-08 05:16  twu

	* src/iitdef.h: Included header file for off_t type.

2005-07-08 05:16  twu

	* src/gmap.c: Changed maxpeelback for cross-species mode back to
	  previous value

2005-07-08 00:45  twu

	* VERSION: Updated version

2005-07-08 00:44  twu

	* configure.ac: Added check for caddr_t type.  Added check for
	  madvise flags.

2005-07-08 00:43  twu

	* src/gmap.c: Removed unnecessary variables and arguments.  Changed
	  variable type of nworkers.

2005-07-08 00:43  twu

	* src/stage2.c: Removed unnecessary variables

2005-07-08 00:42  twu

	* src/: stage1.c, stage1.h: Removed unnecessary arguments

2005-07-08 00:42  twu

	* src/: sequence.c, sequence.h: Added formal void argument.
	  Changed some variable types.

2005-07-08 00:41  twu

	* src/pair.c: Added static specification to some functions

2005-07-08 00:41  twu

	* src/: oligoindex.h, pairpool.c, pairpool.h, stopwatch.c,
	  stopwatch.h: Added formal void argument

2005-07-08 00:39  twu

	* src/: indexdb.c, match.c, segmentpos.c: Changed print statement

2005-07-08 00:39  twu

	* src/: iit-read.c, iitdef.h: Changed some variable types

2005-07-08 00:38  twu

	* src/: compress.c, genome.c, genome.h, matchpair.c, oligoindex.c:
	  Removed unnecessary variables

2005-07-08 00:37  twu

	* src/: block.c, oligo.c, oligo.h, boyer-moore.c, dynprog.c,
	  dynprog.h, matchpair.h: Removed unnecessary arguments

2005-07-07 18:00  twu

	* src/indexdb.c: Increased interval of monitoring output from 1
	  million nt to 10 million nt

2005-07-07 17:59  twu

	* util/gmap_uncompress.pl.in: Fixed bug in argument list

2005-07-07 17:58  twu

	* src/: bigendian.c, boyer-moore.c, chrom.c, chrsubset.c,
	  chrsubset.h, compress.c, datadir.c, dynprog.c, except.c,
	  genome-write.c, genome.c, get-genome.c, gmap.c, gmapindex.c,
	  iit-read.c, iit-write.c, iit_dump.c, iit_get.c, iit_store.c,
	  indexdb.c, interval.h, intlist.c, list.c, match.c, matchpair.c,
	  md5-compute.c, md5.c, mutation.c, oligo-count.c, oligo.c,
	  oligoindex.c, pair.c, pairpool.c, params.h, reqpost.c,
	  segmentpos.c, segmentpos.h, sequence.c, smooth.c, stage1.c,
	  stage2.c, stage3.c, translation.c, uintlist.c: Made changes to
	  satisfy pedantic gcc compiler warnings and to comply with ANSI C

2005-07-07 17:56  twu

	* acinclude.m4: Added autoconf macro for madvise flags

2005-07-07 17:55  twu

	* MAINTAINER: Added comment about strict compiler checking

2005-07-07 17:55  twu

	* config/madvise-flags.m4: Initial import into CVS

2005-07-07 12:34  twu

	* src/gmap.c: Changed parameters to prevent segmentation fault in
	  cross-species mode

2005-07-07 10:01  twu

	* src/: stage3.c, stage3.h: Added psl output format

2005-07-07 10:01  twu

	* src/stage1.c: Increased matchpairs allowed at pre-unique stage

2005-07-07 10:00  twu

	* src/: match.c, match.h: Trivial formatting change

2005-07-07 09:59  twu

	* src/gmapindex.c: Removed some unused variables

2005-07-07 09:59  twu

	* src/get-genome.c: Changed usage statement for coordinate interval

2005-07-07 09:58  twu

	* src/datadir.c: Added error message when genome subdirectory is
	  not readable

2005-07-07 09:57  twu

	* src/: chrnum.c, chrnum.h: Added Chrnum_length command, needed for
	  psl output format

2005-07-07 09:56  twu

	* src/gmap.c: Added psl output format

2005-07-07 09:33  twu

	* src/: pair.c, pair.h: Added psl output format

2005-06-23 09:14  twu

	* VERSION: Updated version for release

2005-06-23 08:49  twu

	* src/stage2.c: Increased cross-species penalty for intron length

2005-06-23 08:49  twu

	* src/gmap.c: Added other constraints on using oligo depth.
	  Reporting failure type.  Separated out beta source files from
	  gmap.

2005-06-23 08:47  twu

	* src/: result.c, result.h: Added failure type

2005-06-23 08:47  twu

	* src/genomeplot.c: Added getopt to genomeplot.  Added mode for
	  printing segments.

2005-06-23 08:46  twu

	* src/: chrsubset.c, chrsubset.h, plotdata.c: Added checks if
	  chrsubset is NULL.

2005-06-23 08:46  twu

	* src/Makefile.am: Added getopt to genomeplot.	Separated out beta
	  source files from gmap.

2005-06-21 04:50  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Fixed coloring of raw
	  data, depending on whether segmentation is performed.

2005-06-21 04:42  twu

	* src/Makefile.am: Moved chrsegment functionality to genomeplot

2005-06-21 04:41  twu

	* src/gmap.c: Giving crossspecies flag to Stage 2

2005-06-21 04:40  twu

	* src/genomeplot.c: Getting segment breakpoints back in three
	  separate lists

2005-06-21 04:39  twu

	* src/: chrsegment.c, chrsegment.h: Added re-checking of segment
	  breakpoints

2005-06-21 04:37  twu

	* src/: intlist.c, intlist.h: Added Intlist_delete function

2005-06-21 04:37  twu

	* src/: stage2.c, stage2.h: Implemented different intron penalties
	  for crossspecies mode

2005-06-21 04:37  twu

	* src/stage1.c: Restored full functionality for crossspecies mode

2005-06-16 10:33  twu

	* src/stage1.c: Added check for too many matchpairs before applying
	  Matchpair_filter_unique

2005-06-16 00:50  twu

	* src/: chrsegment.c, chrsegment.h: Using chromosomal positions in
	  calculations

2005-06-16 00:49  twu

	* src/: genomeplot.c, plotdata.c, plotdata.h: Modified calls to
	  Plotdata_values and Plotdata_chrpositions

2005-06-16 00:05  twu

	* src/: genomeplot.c, iit-read.c, iit-read.h: Added function
	  IIT_length

2005-06-15 23:24  twu

	* src/plotdata.c: Storing chrpositions and values as individual
	  arrays

2005-06-15 23:23  twu

	* src/genomeplot.c: Using a tree structure to store segment
	  results.

2005-06-15 23:23  twu

	* src/: chrsegment.c, chrsegment.h: Using a tree structure to store
	  segment results.  Added check for single breakpoint in addition
	  to double breakpoints.

2005-06-15 10:42  twu

	* src/: chrsegment.c, chrsegment.h, genomeplot.c: Implemented
	  recursive segmentation, generating a list of segments

2005-06-15 10:41  twu

	* src/iit-read.c: Fixed problem with memory fault

2005-06-15 09:23  twu

	* src/: Makefile.am, chrsegment.c, chrsegment.h, genomeplot.c,
	  plotdata.c, plotdata.h: Merged chrsegment functionality into
	  genomeplot

2005-06-15 08:39  twu

	* src/genomeplot.c: Fixed some memory leaks

2005-06-15 08:38  twu

	* src/: datum.c, datum.h: Added Datum_T object for use by
	  Plotdata_T

2005-06-15 08:38  twu

	* src/Makefile.am: Added program chrsegment and added Datum_T
	  object to genomeplot

2005-06-15 08:38  twu

	* src/: chrsegment.c, nr-x.h: Added program chrsegment

2005-06-15 08:36  twu

	* src/: plotdata.c, plotdata.h: Now storing data as sorted within
	  each chromosome

2005-06-15 08:35  twu

	* src/: chrsubset.c, chrsubset.h: Added function to compute and
	  retrieve old indices

2005-06-14 07:43  twu

	* src/: Makefile.am, chrsubset.c, chrsubset.h, color.c, color.h,
	  doublelist.c, doublelist.h, genomeplot.c, plotdata.c, plotdata.h:
	  Added program genomeplot

2005-06-14 07:43  twu

	* src/uintlist.c: Fixed typo

2005-06-14 07:43  twu

	* src/iit-read.c: Skipping freeing of memory, since it sometimes
	  gives a memory fault.

2005-06-14 03:06  twu

	* src/: Makefile.am, chimera.c, maxent.c, maxent.h, splice-site.c,
	  splice-site.h: Changed splice site predictor from scoring matrix
	  to maxent method

2005-06-10 09:59  twu

	* src/indexdb.c: Added error message when user-provided genomic
	  segment is invalid

2005-06-03 06:13  twu

	* src/: chimera.c, chimera.h: Added detection of exon-exon boundary
	  for chimeras in both forward and reverse directions

2005-06-03 06:12  twu

	* src/: pair.c, pair.h, stage3.c, stage3.h, gmap.c: Added output of
	  cDNA direction of exon-exon boundary for chimeras

2005-06-02 10:27  twu

	* src/: stage3.c, gmap.c, dynprog.c, dynprog.h: Restored previous
	  behavior for finding microexons.  Changed meaning of
	  end_microexons_p to be an allowance for longer introns at the
	  ends.

2005-06-02 10:26  twu

	* src/chimera.c: Improved debugging output

2005-06-01 08:19  twu

	* src/: stage3.c, stage3.h: Added utilities for new chimera
	  functions.

2005-06-01 08:18  twu

	* src/gmap.c: Added stage 3 calls for truncating full length.
	  Using Chimera_T objects and new chimera functions.

2005-06-01 08:15  twu

	* src/: stage1.c, stage1.h: Using ends only for cross-species mode
	  in stage 1

2005-06-01 08:15  twu

	* src/: result.c, result.h: Created Chimera_T object.

2005-06-01 08:14  twu

	* src/: pair.c, pair.h: Added utility programs for chimera
	  evaluation.

2005-06-01 08:14  twu

	* src/: chimera.c, chimera.h: Added search for exon-exon boundaries
	  in chimeras.	Created Chimera_T object.

2005-06-01 08:13  twu

	* src/: Makefile.am, splice-site.c, splice-site.h: Added splice
	  site calculations to chimera evaluation.

2005-05-24 16:41  twu

	* src/gmap.c: Moved translate calls up to gmap.c.  Added hook for
	  -T flag for truncating full-length sequence.

2005-05-24 16:40  twu

	* src/: stage3.c, stage3.h: Using function
	  Pairpool_transfer_bounded.  Moved translate calls up to gmap.c.

2005-05-24 16:39  twu

	* src/: pairpool.c, pairpool.h: Added function
	  Pairpool_transfer_bounded.

2005-05-20 03:43  twu

	* VERSION: Revised version

2005-05-20 03:42  twu

	* src/: stage3.c, stage3.h: Turned off default microexon finding at
	  ends.  Cleaned up margin function for identifying chimeras.

2005-05-20 03:41  twu

	* src/pair.c: Changed computation of matchscores

2005-05-20 03:40  twu

	* src/oligoindex.c: Changed definition of oligodepth.

2005-05-20 03:40  twu

	* src/gmap.c: Added -U flag to turn on microexons at ends.  Changed
	  code for chimeras, and changed meaning of -x flag.

2005-05-20 03:38  twu

	* src/chrsubset.c: Added check on freeing object.

2005-05-20 03:37  twu

	* src/chimera.c: Fixed debugging statement

2005-05-20 03:37  twu

	* src/Makefile.am: Added beta testing flag.

2005-05-09 12:51  twu

	* src/Makefile.am: Added compiler instructions for pthreads to
	  various programs

2005-05-09 12:26  twu

	* VERSION: Modified version number.

2005-05-09 12:26  twu

	* README: Added information about -E feature of fa_coords and
	  gmap_setup, and information about editing coords.txt.

2005-05-09 12:20  twu

	* MAINTAINER: Added reminder to modify VERSION.

2005-05-09 12:19  twu

	* util/gmap_setup.pl.in: Removed reverse complement procedures
	  here; now being done by gmapindex.  Allowed specification of a
	  command.

2005-05-09 12:18  twu

	* util/fa_coords.pl.in: Introduced chromosome NA for headers that
	  cannot be parsed.  Allowed specification of a command.  Improved
	  handling of Celera genomes.

2005-05-09 12:14  twu

	* src/: genome.c, indexdb.c: Put mutexes around read procedures for
	  the combination of multi-threading and non-memory mapped reading
	  of file.

2005-05-09 12:13  twu

	* src/gmap.c: Fixed bug from uninitialized querysubseq.

2005-05-09 08:33  twu

	* src/: pair.c, pair.h, result.c, result.h, stage3.c, stage3.h:
	  Allowed printing of range of chimera breakpoints

2005-05-09 08:33  twu

	* src/: interval.c, interval.h: Changed interface to some functions

2005-05-09 08:32  twu

	* src/: iit-read.c, iit-write.c: Fixed bug in debug version of
	  dump.  Changed calls to Interval_T functions.

2005-05-09 08:29  twu

	* src/gmapindex.c: Changed count_sequence() to read a line at a
	  time

2005-05-09 08:28  twu

	* src/genome-write.c: Properly handling contigs marked as reverse
	  complement.

2005-05-09 08:27  twu

	* src/gmap.c: Using fscore threshold to determine statistical
	  significance.  Reporting equivalent positions for breakpoint.

2005-05-09 08:26  twu

	* src/: chimera.c, chimera.h: Using fscore threshold to determine
	  statistical significance

2005-05-06 07:50  twu

	* util/gmap_setup.pl.in: Handling other NCBI cases where version
	  numbers are missing

2005-05-06 07:20  twu

	* src/: genome-write.c, indexdb.c: Minor changes in monitoring
	  output

2005-05-06 07:11  twu

	* VERSION: Updated version number

2005-05-06 06:55  twu

	* README: Added explanation of output ordering with multiple
	  threads

2005-05-06 06:52  twu

	* tests/coords1.test.ok: Changed to add new comment line in
	  coords.txt

2005-05-06 06:51  twu

	* README: Minor textual change

2005-05-06 06:34  twu

	* util/gmap_setup.pl.in: Added -q flag for specifying indexing
	  interval.  Allowed comment lines to be in coords.txt.

2005-05-06 06:33  twu

	* util/md_coords.pl.in: Improved messages to user.

2005-05-06 06:33  twu

	* util/fa_coords.pl.in: Added handling of unmapped contigs for
	  Ensembl genomes.  Improved messages to user.	Added check for
	  possible conversions of alternate chromosomes to alternate
	  strains.

2005-05-06 05:08  twu

	* util/gmap_uncompress.pl.in: Fixed bug due to old code that
	  referred to the -R flag

2005-05-06 04:46  twu

	* src/gmap.c: Enhanced result to show number of matches,
	  mismatches, and indels in alternative to chimera.  Introduced
	  maxpaths of 0 to indicate output of both paths of chimera if
	  present, otherwise one path.

2005-05-06 04:44  twu

	* src/: stage3.c, stage3.h, pair.c, pair.h, sequence.c, sequence.h:
	  Removed references to ntrimmed

2005-05-06 04:44  twu

	* src/: result.c, result.h: Enhanced result to show number of
	  matches, mismatches, and indels in alternative to chimera

2005-05-06 03:04  twu

	* src/gmap.c: Remove check for badoligos.  Modified logic for
	  computing chimeras.  Made calls to initialization and termination
	  routines for Dynprog_T.

2005-05-06 03:03  twu

	* src/chimera.c: Fixed memory leak

2005-05-06 03:02  twu

	* src/pair.c: Removed printing of ntrimmed nucleotides

2005-05-06 03:01  twu

	* src/: stage3.c, stage3.h: Added functions for reporting matches,
	  mismatches, indels, and margin of a Stage3_T object

2005-05-06 03:00  twu

	* src/translation.c: Added initial values for translation_start and
	  translation_end

2005-05-06 03:00  twu

	* src/stage2.c: Removed computation of stage2 support.	Simplified
	  loop conditions.

2005-05-06 02:59  twu

	* src/: oligoindex.c, oligoindex.h: Removed computation of stage2
	  support

2005-05-06 02:59  twu

	* src/: dynprog.c, dynprog.h: Replaced functions with arrays for
	  computing pairdistances and jump penalties

2005-05-05 11:09  twu

	* src/: oligoindex.c, oligoindex.h: Changed memory allocation
	  scheme, by setting ALLOCSIZE == MAXHITS.  Assigning blocks in
	  ascending order of available slots.  Computing trim_start and
	  trim_end.  Reporting support for stage 2.

2005-05-05 11:06  twu

	* src/gmap.c: Changed calls to Sequence_read().  Using
	  oligomer-based method for trimming query sequence.

2005-05-05 11:02  twu

	* src/: md5-compute.c, oligo-count.c: Changed calls to
	  Sequence_read()

2005-05-05 11:02  twu

	* src/: sequence.c, sequence.h: Removed poly-A and poly-T detection
	  in favor of oligomer-based trimming at ends.

2005-05-05 09:45  twu

	* src/: stage2.c, stage2.h: Added check for stage 2 support.

2005-05-05 09:44  twu

	* src/stage1.c: Restored terminal sampling for short sequences.
	  Fixed potential bug with subtracting unsigned ints.  Enhanced
	  debugging messages.

2005-05-05 09:43  twu

	* src/: sequence.c, sequence.h, md5-compute.c, oligo-count.c:
	  Modified functions to report next char in input.

2005-05-05 09:43  twu

	* src/: matchpair.c, matchpair.h: Added reporting of stage1 support
	  and stage1 stretch.

2005-05-05 09:42  twu

	* src/gmap.c: Added checks for bad input sequences based on oligo
	  depth, bad oligos, stage1 support, and stage2 support.  Moved
	  message about batch mode earlier, if evidence of a second
	  sequence is present.

2005-05-04 23:38  twu

	* src/gmap.c: Chopping chimeras at breakpoint, and providing a flag
	  to allow overlaps at the breakpoint.

2005-05-04 23:37  twu

	* src/: stage3.c, stage3.h: Simplified interface to Stage3_copy.

2005-05-04 23:36  twu

	* src/: pair.c, pair.h: Removed coverage correction for genomic
	  gaps.  Added way to turn off merge_gaps during copying of pairs.

2005-05-04 16:58  twu

	* src/stage2.c: Made changes in individual instructions to improve
	  speed

2005-05-04 16:57  twu

	* src/oligoindex.c: Added overabundant field

2005-05-04 16:56  twu

	* src/chimera.c: Speeded up computation

2005-05-04 15:16  twu

	* src/gmap.c: Using explicit step for marking oligos in the query.
	  Terminating attempt at mapping if oligo depth exceeds 2.  Fixed
	  memory leak.

2005-05-04 15:14  twu

	* src/: stage2.c, stage2.h: The variable badsequencep is now fed
	  into Stage2_compute.

2005-05-04 15:14  twu

	* src/stage1.c: Killed terminal sampling for short sequences.
	  Reduced values for maxentries.  Both done to improve speed.

2005-05-04 15:13  twu

	* src/: oligoindex.c, oligoindex.h: Added an explicit step for
	  marking oligos in the query, which needs to be done only once for
	  each query sequence.

2005-05-04 09:50  twu

	* src/chimera.h: Added computation of margin.

2005-05-04 09:50  twu

	* src/chimera.c: Added computation of margin.  Improved debugging
	  output.

2005-05-04 09:49  twu

	* src/gmap.c: Fixed bug where bestfrom == bestto.  Added check for
	  sufficient margin at ends before finding chimera.

2005-05-04 05:11  twu

	* util/gmap_compress.pl.in: Changed compression routine to handle
	  chimera information

2005-05-04 04:49  twu

	* src/chrsubset.c: Fixed bug where stdin was closed if .chrsubset
	  file didn't exist

2005-05-04 04:20  twu

	* src/stage3.h: Added function to compute matchscores for chimera
	  detection.

2005-05-04 04:20  twu

	* src/stage3.c: Changed calls to Sequence_T functions.	Added
	  function to compute matchscores for chimera detection.

2005-05-04 04:19  twu

	* src/stage2.c: Performing Stage 2 from trim start to trim end,
	  instead of entire sequence.  Changed calls to Sequence_T
	  functions.

2005-05-04 04:18  twu

	* src/stage1.c: Changed calls to Sequence_T and Reader_T functions

2005-05-04 04:08  twu

	* src/: sequence.c, sequence.h: Cleaned up interface.  Added
	  ability to print trimmed part of sequence.

2005-05-04 04:07  twu

	* src/: pair.c, pair.h: Added chimera detection based on Chow test

2005-05-04 04:06  twu

	* src/md5-compute.c: Changed call to Sequence_T function.  Using
	  full sequence now for MD5 computation.

2005-05-04 04:06  twu

	* src/matchpair.c: Removed call to Sequence_T function

2005-05-04 04:05  twu

	* src/oligoindex.c: Changed calls to Sequence_T functions

2005-05-04 04:05  twu

	* src/oligo-count.c: Changed call to Reader_new

2005-05-04 04:04  twu

	* src/get-genome.c: Changed call to Sequence_print

2005-05-04 04:04  twu

	* src/: reader.c, reader.h: Storing querystart and queryend in
	  Reader_T object

2005-05-04 04:03  twu

	* src/: block.c, block.h: Removed unnecessary field

2005-05-04 04:02  twu

	* src/: Makefile.am, chimera.c, chimera.h, nmath.c, nmath.h,
	  gmap.c: Added chimera detection based on Chow test

2005-05-03 03:25  twu

	* src/: gmap.c, gmapindex.c, indexdb.c, indexdb.h: Allowed indexing
	  interval of 12-mers to be specified at run time

2005-05-03 02:58  twu

	* configure.ac: Added check for madvise function

2005-05-03 02:56  twu

	* README: Added Ensembl format as a recognized coordinate format

2005-05-03 02:55  twu

	* util/md_coords.pl.in: Improved prompt for alternate chromosomes

2005-05-03 02:49  twu

	* src/: genome.c, iit-read.c, indexdb.c: Put compiler flags around
	  madvise

2005-05-03 02:48  twu

	* src/datadir.c: Deleted line that was causing problems when the
	  GMAPDB environment variable was set

2005-05-01 02:20  twu

	* util/fa_coords.pl.in: Further fixed coordinates

2005-05-01 01:53  twu

	* util/fa_coords.pl.in: Removed addition of 1 to coordinates.
	  Added parsing for Ensembl format.

2005-05-01 01:16  twu

	* util/gmap_setup.pl.in: Testing accessions with and without
	  version numbers

2005-05-01 01:15  twu

	* util/md_coords.pl.in: Making -U and -A flags standard.  Can
	  exclude unmapped contigs and alternate chromosomes with
	  chrsubsets.

2005-05-01 01:13  twu

	* util/md_coords.pl.in: Fixed case where direction eq "0".

2005-05-01 00:52  twu

	* src/oligoindex.c: Modified memory allocation scheme to have a
	  fixed block of memory that expands when necessary.

2005-05-01 00:51  twu

	* src/iit_get.c: Added -A back to allowed flags.

2005-05-01 00:49  twu

	* src/chrsubset.c: Added debug statements

2005-05-01 00:48  twu

	* VERSION: Updated version

2005-04-20 04:12  twu

	* src/sequence.c: Kept poly-A and poly-T limits when specifying
	  subsequences.

2005-04-20 04:11  twu

	* src/pair.c: Added an exception handler.  Removed minor bug where
	  first pair was handled twice.

2005-04-20 04:10  twu

	* src/gmapindex.c: Allowed compress and uncompress routines to take
	  a filename as an argument.  Added wraplength option for
	  uncompress.

2005-04-20 04:10  twu

	* src/gmap.c: Fixed bug in specifying wrong sequence length for
	  computing chimeras.  Removed limit on number of paths for finding
	  chimeras.  Added exception handler.

2005-04-20 04:08  twu

	* src/except.c: Modified behavior of exception handler

2005-04-20 04:07  twu

	* src/genuncompress.c: Fixed problem if positions were greater than
	  allowed for signed ints.

2005-04-20 04:06  twu

	* src/: compress.c, compress.h: Added wraplength option to
	  Compress_uncompress.

2005-04-19 01:51  twu

	* src/: sequence.c, stage1.c: Added checks for null before freeing
	  memory.

2005-04-19 01:51  twu

	* src/gmap.c: Made IIT_get return an array of ints, rather than an
	  Intlist, to reduce repeated small memory allocations.  Placed a
	  limit on npaths for finding chimeras.

2005-04-19 01:50  twu

	* src/: get-genome.c, iit-read.c, iit-read.h, iit_get.c,
	  segmentpos.c, stage3.c: Made IIT_get return an array of ints,
	  rather than an Intlist, to reduce repeated small memory
	  allocations.

2005-04-19 01:48  twu

	* src/mem.c: Added debugging statements.

2005-04-18 06:05  twu

	* src/dynprog.c: Added memory allocation routines in cases where
	  problem size exceeds maxlength of Dynprog_T.	Removed unused code
	  for affine gap penalties.

2005-03-11 01:58  twu

	* util/: gmap_setup.pl.in, md_coords.pl.in: Allowed for contigs to
	  be reverse complement

2005-03-11 01:57  twu

	* util/fa_coords.pl.in: Removed unused functions

2005-03-11 01:56  twu

	* src/gmap.c: Moved dump functions to get-genome

2005-03-11 01:56  twu

	* src/segmentpos.c: Fixed bug when alternate strain contig exists
	  but reference is to reference strain

2005-03-11 01:55  twu

	* src/: get-genome.c, iit-read.c, iit-read.h: Changed output of
	  dump functions

2005-03-11 01:34  twu

	* src/get-genome.c: Moved dump functions to get-genome

2005-03-11 01:33  twu

	* README: Added instructions for specifying reverse coordinates

2005-03-11 01:33  twu

	* VERSION: Changed version number

2005-03-09 03:25  twu

	* src/: gmapindex.c, iit-read.c: Now storing information about
	  reverse complementing of contigs

2005-03-09 03:23  twu

	* src/: get-genome.c, gmap.c: Fixed bug when using the -R release
	  flag.

2005-03-09 03:23  twu

	* src/: match.c, pair.c, pair.h, stage3.c, segmentpos.c,
	  segmentpos.h: Limited printing of contigs to those that are
	  relevant for a given strain.

2005-03-08 02:45  twu

	* src/get-genome.c: Changed default behavior to print just the
	  reference strain.  Added a flag to print all strains.

2005-03-04 06:38  twu

	* src/chrsubset.c: Fixed minor memory leak

2005-03-04 06:32  twu

	* VERSION: Updated version

2005-03-04 06:31  twu

	* README: Added explanation of chromosome subsets

2005-03-04 06:02  twu

	* src/chrsubset.c: Changed Chrsubset_T object to be NULL when a
	  blank list is read in .chrsubset file.

2005-03-04 06:01  twu

	* src/gmap.c: Incorporated chrsubset.  Fixed printing of option
	  flags.

2005-03-04 04:49  twu

	* util/gmap_setup.pl.in: Added creation of chrsubset file

2005-03-04 04:48  twu

	* util/whats_on: Changed directories where genomic maps are located

2005-03-04 04:48  twu

	* src/: Makefile.am, chrsubset.c, chrsubset.h, params.c, params.h,
	  stage1.c, stage1.h: Added capability to search on chromosome
	  subsets

2005-03-04 04:47  twu

	* src/separator.h: Changed separator back to dashes

2005-03-04 04:47  twu

	* src/iit-read.c: Changed format of dumping typestrings for
	  .altstrain.type file.

2005-03-04 04:47  twu

	* src/gmapindex.c: Added writing of .altstrain.type file.

2005-03-04 00:38  twu

	* src/stage1.c: Removed unused code.  Using stage1size instead of
	  INDEX1PART in some places.

2005-03-04 00:37  twu

	* src/gmap.c: Added error message.

2005-03-04 00:37  twu

	* src/datadir.c: Removed unused error message.

2005-03-03 07:44  twu

	* src/stage1.c: Introduced idea of dangling matches at ends, and
	  using it to determine when to sample further at each end, and
	  when to sample from the middle.

2005-03-02 09:34  twu

	* src/separator.h: Changed separator from dashes to dots.

2005-03-02 03:19  twu

	* src/stage1.c: Fixed a bug in find_3prime_matches.  Changed
	  sampling to avoid terminal sampling, and to redo sampling just
	  before nskip is zero.  This is done to avoid long computation
	  times with terminal sampling on long cDNAs.

2005-03-01 04:22  twu

	* src/: matchpair.c, matchpair.h: Added a boundmethod type.

2005-03-01 04:21  twu

	* src/stage1.c: Added code for finding matches using triplets, but
	  not using it.  Removing terminal sampling, and performing a redo
	  of last sampling instead.

2005-02-18 08:45  twu

	* src/: params.c, params.h: Removed maxintronlen from the params
	  structure.

2005-02-18 08:45  twu

	* src/gmap.c: Increased default maxintronlen to 1.2M, and provided
	  a flag to allow user to change this value.

2005-02-18 03:16  twu

	* config/perl.m4, configure.ac: Changed name of macro

2005-02-18 01:51  twu

	* configure.ac: Added check for Perl with needed modules.  Added
	  warning messages to bottom of configure script.

2005-02-18 01:51  twu

	* config.site: Added option for user to specify a value for PERL

2005-02-18 01:50  twu

	* acinclude.m4: Added check for Perl with needed modules

2005-02-18 01:49  twu

	* config/perl.m4: Added check for Perl with appropriate modules

2005-02-18 00:10  twu

	* VERSION: Set version number

2005-02-18 00:07  twu

	* README: Removed optional comment after make check

2005-02-18 00:07  twu

	* COPYING, config.site: Changed wording slightly

2005-02-17 06:41  twu

	* src/datadir.c, util/gmap_setup.pl.in: Allowed subdirectory to be
	  present in the -d flag

2005-02-17 06:40  twu

	* config.site: Fixed advice on installing in build directory

2005-02-17 06:37  twu

	* README: Fixed some textual errors

2005-02-16 06:41  twu

	* util/gmap_setup.pl.in: Modified instruction text

2005-02-16 05:15  twu

	* util/md_coords.pl.in: Added guessing of columns

2005-02-16 03:23  twu

	* src/: genome.c, genuncompress.c, iit-read.c, indexdb.c: Added
	  type cast to avoid compiler warnings for munmap.

2005-02-16 03:03  twu

	* configure.ac: Removed capitalization

2005-02-16 03:02  twu

	* VERSION: Updated version

2005-02-16 03:01  twu

	* configure.ac: Capitalized message when compilation of pthreads
	  fails

2005-02-16 03:00  twu

	* Makefile.am: Added subdirectories

2005-02-16 02:52  twu

	* tests/: iit_get.out.ok, iittest.iit.ok: Added okay files for IIT
	  programs

2005-02-16 02:50  twu

	* AUTHORS: Minor text change

2005-02-16 02:49  twu

	* util/gmap_setup.pl.in: Changed usage statement

2005-02-16 02:49  twu

	* config/acx_pthread.m4: Updated macro to latest version

2005-02-16 02:48  twu

	* configure.ac: Added tests for IIT programs.  Changed call to
	  ACX_PTHREAD.

2005-02-16 02:48  twu

	* config.site.gne: Changed name from genomedir to gmapdb

2005-02-16 02:48  twu

	* config.site: Added lines for PTHREAD_CFLAGS and PTHREAD_LIBS

2005-02-16 02:47  twu

	* MAINTAINER: Added instructions for building .ok files for tests

2005-02-16 02:47  twu

	* tests/: align.test.in, coords1.test.in, map.test.in,
	  setup1.test.in, setup2.test.in: Added ${srcdir} where necessary
	  to make distcheck happy

2005-02-16 02:45  twu

	* tests/: Makefile.am, fa.iittest, iit.test.in, iit_dump.test.in,
	  iit_get.test.in, iit_store.test.in: Added tests for IIT programs

2005-02-16 02:45  twu

	* src/gmap.c: Changed ENABLE_PTHREADS to HAVE_PTHREAD.	Added
	  reporting of features to version command.

2005-02-16 02:44  twu

	* src/: blackboard.c, reqpost.c: Changed ENABLE_PTHREADS to
	  HAVE_PTHREAD

2005-02-16 02:44  twu

	* src/iit_store.c: Changed flags and calling convention

2005-02-16 02:44  twu

	* src/Makefile.am: Removed ENABLE_PTHREADS and POPT_LIBS.

2005-02-16 02:43  twu

	* acinclude.m4: Changed name of file

2005-02-16 02:43  twu

	* README: Completed instructions

2005-02-16 02:42  twu

	* COPYING: Completed license terms

2005-02-16 01:19  twu

	* config/: acx-pthread.m4, acx_pthread.m4: Changed name of file

2005-02-16 01:16  twu

	* config/acx-pthread.m4, config/expand.m4, config/mmap-flags.m4,
	  config/pagesize.m4, acinclude.m4: Put m4 macros into separate
	  files

2005-02-15 22:49  twu

	* configure.ac: Commented out code for AC_PROG_LIBTOOL.  Added some
	  compiler checks.

2005-02-15 08:45  twu

	* util/gmap_setup.pl.in: Removed IO::Dir.  Changed behavior if -I
	  flag not given.  Added -9 for debugging behavior.

2005-02-15 08:44  twu

	* util/: fa_coords.pl.in, md_coords.pl.in: Removed IO::Dir

2005-02-15 08:44  twu

	* src/: iit-read.h, iit-write.h: Fixed compiler complaint about
	  double typedef for IIT_T

2005-02-15 08:43  twu

	* src/iit-read.c: Fixed one-off problem with IIT_totallength.

2005-02-15 08:43  twu

	* src/genome-write.c: Fixed montoring statements.

2005-02-15 08:42  twu

	* src/gmap.c: Put pthreads information in version text.

2005-02-15 08:42  twu

	* src/gmapindex.c: Fixed problem in comparing an int (255) with EOF
	  (-1) on some machines.

2005-02-15 04:39  twu

	* tests/: Makefile.am, align.test.in, align.test.ok,
	  coords1.test.in, coords1.test.ok, map.test.in, map.test.ok,
	  setup.genomecomp.ok, setup.idxpositions.ok, setup1.test.in,
	  setup2.test.in, ss.chr17test: Expanded test suite

2005-02-15 01:01  twu

	* tests/: Makefile.am, ss.cdna, ss.chr17test, ss.her2: Initial
	  addition to CVS repository.

2005-02-14 10:01  twu

	* util/: gmap_setup.pl.in, md_coords.pl.in: Moved functionality to
	  separate md_coords program

2005-02-14 10:00  twu

	* util/Makefile.am: Added fa_coords program

2005-02-14 10:00  twu

	* util/fa_coords.pl.in: Added file to CVS repository.

2005-02-14 09:58  twu

	* src/: block.c, block.h, compress.c, dynprog.c, dynprog.h,
	  genome-write.c, iit-read.c, iit-write.c, indexdb.c, interval.c,
	  intron.c, match.c, match.h, matchpair.c, matchpair.h, md5.c,
	  md5.h, md5.t.c, oligo.c, oligo.h, pair.h, pairpool.c, pairpool.h,
	  reader.c, request.c, result.h, segmentpos.c, segmentpos.h,
	  smooth.c, smooth.h, stage1.c, stage3.c, stopwatch.c,
	  translation.h: Cleaned up included headers

2005-02-14 09:57  twu

	* src/: table.c, tableint.c, table.h, tableint.h: Clarified meaning
	  of unsigned type.

2005-02-14 09:56  twu

	* src/reqpost.h: Using Blackboard_T in interface.

2005-02-14 09:56  twu

	* src/oligo-count.c: Fixed call to Block_new.

2005-02-14 09:55  twu

	* src/listdef.h: Added a define for T.

2005-02-14 09:55  twu

	* src/iitdef.h: Moved typedef to iit-read.h and iit-write.h.

2005-02-14 09:55  twu

	* src/iit_get.c: Removed popt library calls.

2005-02-14 09:54  twu

	* src/: iit-read.h, iit-write.h: Moved include of iitdef.h to .c
	  files.

2005-02-14 09:54  twu

	* src/get-genome.c: Using SEPARATOR now instead of DASH.

2005-02-14 09:53  twu

	* src/: datadir.c, datadir.h: Formatting changes.

2005-02-14 09:52  twu

	* src/: gmap.c, oligoindex.c, oligoindex.h, params.c, params.h,
	  stage2.c, stage2.h: Moved get_mappings command to be in
	  oligoindex.c.  Moved indexsize to be stored in Params_T.

2005-02-14 09:50  twu

	* src/: complement.c, complement.h, genome.c, pair.c, sequence.c,
	  translation.c: Changed complement table to be a macro.

2005-02-14 09:26  twu

	* src/: chrom.h, chrom.c: Clarified meaning of unsigned type.

2005-02-14 09:25  twu

	* src/blackboard.h: Added comments about include of reqpost.h.

2005-02-14 09:25  twu

	* src/Makefile.am: Cleaned up source files needed for each binary.

2005-02-14 09:24  twu

	* src/shortoligomer.h: Removed file.  Definition needed only by
	  oligoindex.c.

2005-02-13 21:01  twu

	* src/iit-read.h: Added function to compute total length.

2005-02-13 21:01  twu

	* src/iit-read.c: Conditionally include littleendian.h.  Added
	  function to compute total length.

2005-02-13 21:01  twu

	* src/indexdb.h: Allow user to force building of positions file in
	  file.

2005-02-13 21:00  twu

	* src/indexdb.c: Conditionally include littleendian.h.	Allow user
	  to force building of positions file in file.

2005-02-13 21:00  twu

	* src/: iit-write.c, littleendian.h, genuncompress.c, bigendian.h:
	  Conditionally include littleendian.h.

2005-02-13 20:59  twu

	* src/genome-write.c: Added explanation of file format.

2005-02-13 20:59  twu

	* src/genome.c: Changed type from unsigned int to UINT4.
	  Conditionally include littleendian.h.

2005-02-13 20:51  twu

	* src/: compress.c, compress.h: Added ability to create genome file
	  in memory, if enough is available.  Changed type from unsigned
	  int to UINT4.

2005-02-13 20:50  twu

	* src/: Makefile.am, genome-write.c, genome-write.h, gmapindex.c:
	  Moved procedures for writing genome file to a new file.  Added
	  ability to create genome file in memory, if enough is available.

2005-02-10 01:39  twu

	* src/iit_get.c: Added include for strings.h to handle rindex.

2005-02-10 01:37  twu

	* src/: bigendian.h, genome.c, genuncompress.c, indexdb.c,
	  sequence.c: Added includes for stddef.h to handle size_t

2005-02-10 01:09  twu

	* src/: genome.c, genuncompress.c, iit-read.c, indexdb.c: Added
	  check for HAVE_SYS_STAT_H

2005-02-10 01:08  twu

	* src/: gmap.c, gmapindex.c, oligo-count.c: Removed include of
	  sys/stat.h

2005-02-10 01:02  twu

	* src/iit-read.c: Commented out include of sys/param.h

2005-02-10 01:01  twu

	* src/: genome.c, indexdb.c: Commented out include of errno.h

2005-02-10 00:58  twu

	* src/except.c: Removed code for mailing error messages to
	  developer.

2005-02-10 00:28  twu

	* src/: genome.c, genuncompress.c, gmapindex.c, iit-read.c,
	  iit_store.c, indexdb.c, md5-compute.c, stopwatch.c: Added checks
	  for HAVE_UNISTD_H and HAVE_FCNTL_H.

2005-02-10 00:17  twu

	* src/: blackboard.c, compress.c, datadir.c, genome.c,
	  genuncompress.c, gmap.c, gmapindex.c, iit-read.c, iit_store.c,
	  indexdb.c, oligo-count.c, reqpost.c, stopwatch.c: Added check for
	  HAVE_SYS_TYPES_H

2005-02-10 00:04  twu

	* src/: genome.c, genomicpos.c, iit-write.c, indexdb.c, match.c,
	  md5.c, oligoindex.c, pair.c, sequence.c: Created separate macros
	  for handling absence of memcpy and memmove.

2005-02-09 23:59  twu

	* src/: genome.c, genomicpos.c, iit-write.c, indexdb.c, match.c,
	  md5.c, oligoindex.c, pair.c, sequence.c: Included macros for
	  handling computers without memcpy or memmove.

2005-02-09 23:59  twu

	* src/datadir.c: Included macros for handling computers without
	  dirent.h.

2005-02-07 08:02  twu

	* src/: chimera.c, translation.c: Fixed rcsid lines

2005-02-07 08:01  twu

	* src/: Makefile.am, uinttable.c, uinttable.h: Removed files
	  uinttable.c and uinttable.h

2005-02-07 08:00  twu

	* src/bigendian.c: Added ending quotation mark to rcsid.

2005-02-07 08:00  twu

	* src/: bigendian.h, chimera.h, scores.h, separator.h: Added Id
	  comment to beginning of header files.

2005-02-07 07:56  twu

	* src/: assert.c, assert.h, bigendian.c, bigendian.h, blackboard.c,
	  blackboard.h, block.c, block.h, boyer-moore.c, chimera.c,
	  chrnum.c, chrnum.h, chrom.c, chrom.h, complement.c, complement.h,
	  compress.c, datadir.h, dynprog.c, dynprog.h, except.c, except.h,
	  genome.c, genome.h, genomicpos.c, genomicpos.h, get-genome.c,
	  gmap.c, gmapindex.c, iit-read.c, iit-read.h, iit-write.c,
	  iit-write.h, iit_dump.c, iit_get.c, iit_store.c, indexdb.c,
	  indexdb.h, interval.c, interval.h, intlist.c, intlist.h,
	  intron.c, intron.h, list.c, list.h, match.c, match.h,
	  matchpair.c, matchpair.h, md5-compute.c, md5.c, md5.h, mem.c,
	  mem.h, mutation.c, mutation.h, oligo-count.c, oligo.c, oligo.h,
	  oligoindex.c, oligoindex.h, pair.c, pair.h, pairpool.c,
	  pairpool.h, params.c, params.h, reader.c, reader.h, reqpost.c,
	  reqpost.h, request.c, request.h, result.c, result.h,
	  segmentpos.c, segmentpos.h, sequence.c, sequence.h, smooth.c,
	  smooth.h, stage1.c, stage1.h, stage2.c, stage2.h, stage3.c,
	  stage3.h, stopwatch.c, stopwatch.h, table.c, table.h, tableint.c,
	  tableint.h, translation.c, translation.h, uintlist.c, uintlist.h,
	  uinttable.c, uinttable.h: Moved HAVE_CONFIG_H from .h file to .c
	  file.

2005-02-07 07:55  twu

	* src/datadir.c: Added check to see if closedir succeeded.

2005-02-07 07:19  twu

	* src/Makefile.am: Augmented list of bin programs.

2005-02-07 07:19  twu

	* src/get-genome.c: Changing variable names to genomesubdir,
	  fileroot, and dbversion.

2005-02-07 07:08  twu

	* src/gmap.c: Added -g flag.  Changing variable names to
	  genomesubdir, fileroot, and dbversion.

2005-02-07 07:08  twu

	* src/: params.c, params.h: Made dbversion a static variable.

2005-02-07 07:06  twu

	* src/: match.c, pair.c, pair.h, stage3.c, stage3.h: Changing
	  variable names to genomesubdir, fileroot, and dbversion.

2005-02-07 07:06  twu

	* src/: genome.c, genome.h, indexdb.c, indexdb.h: Changing variable
	  names to genomesubdir and fileroot.

2005-02-07 07:04  twu

	* src/: datadir.c, datadir.h: Now searching subdirectory to find
	  name of fileroot, which can be different from subdirectory name.

2005-02-07 03:05  twu

	* src/pair.c: Removed unnecessary math.h header.  Added
	  initialization of donor and acceptor arrays.

2005-02-07 03:05  twu

	* src/getopt.c: Removed internationalization code.

2005-02-07 03:04  twu

	* src/gmap.c: Removed unnecessary math.h header.  Changed location
	  of map directory for each genome.

2005-02-07 03:03  twu

	* src/: matchpair.c, oligoindex.c, segmentpos.c, smooth.c,
	  stage3.c: Removed unnecessary math.h header.

2005-02-07 03:03  twu

	* src/: indexdb.c, indexdb.h: Allowed user to build positions file
	  directly to disk, if sufficient memory is unavailable.

2005-02-07 03:02  twu

	* src/: mem.c, mem.h: Added procedures for allocating memory
	  without throwing an exception.

2005-02-07 03:01  twu

	* src/gmapindex.c: Changed flags.  Allowed user to build positions
	  file directly to disk, if sufficient memory is unavailable.

2005-02-07 02:58  twu

	* src/chrom.c: Eliminated printing of initial zero on non-numeric
	  chromosomes.

2005-02-03 05:18  twu

	* util/gmap_setup.pl.in: Removed -R flag, and symbolic links.
	  Fixed problems with parsing unmapped contigs in seq_contig.md
	  files.

2005-02-03 01:07  twu

	* src/gmapindex.c: Added debugging statements.

2005-01-27 08:39  twu

	* config.site: Added warning about non-absolute paths.

2005-01-27 08:39  twu

	* README: Added comments about downloading a genome database.

2005-01-27 08:38  twu

	* Makefile.am: Added extra commands for "make distcheck" to be
	  happy.  Removed genome example.

2005-01-27 08:38  twu

	* MAINTAINER: Added comment about --enable-fulldist

2005-01-26 13:54  twu

	* src/datadir.c, src/Makefile.am, config.site, configure.ac:
	  Changed GENOMEDIR to GMAPDB.

2005-01-25 08:48  twu

	* tests/: ss.AA005326, ss.cdna: Changed name of example cDNA
	  sequence.

2005-01-24 14:22  twu

	* MAINTAINER: Added recommended steps for creating a distribution.

2005-01-24 14:21  twu

	* src/: Makefile.am, chrnum.c, chrnum.h, chrom.c, chrom.h,
	  genome.c, genome.h, get-genome.c, gmap.c, gmapindex.c, match.c,
	  match.h, matchdef.h, matchpair.c, pair.c, pair.h, segmentpos.c,
	  segmentpos.h, stage1.c, stage3.c, stage3.h: Made changes to allow
	  chromosome names to be arbitrarily long

2005-01-24 14:20  twu

	* util/gmap_setup.pl.in: Removed restriction on chromosome name
	  length.  Stripped spaces from beginning and end of input.  Added
	  step to create initial genomedir.

2005-01-24 06:51  twu

	* config.site: Changed defaults in config.site.

2005-01-24 06:44  twu

	* src/: getopt.c, getopt.h, getopt1.c: Added gnu getopt_long
	  function

2005-01-24 06:30  twu

	* tests/ss.AA005326: Added test sequence.

2005-01-24 06:19  twu

	* util/Makefile.am: Created Makefile.am in util subdirectory

2005-01-24 06:14  twu

	* src/: Makefile.am, get-genome.c, gmap.c: Added gnu getopt_long
	  procedure

2005-01-24 06:14  twu

	* README: Changed prerequisites.  Improved formatting.

2005-01-24 06:14  twu

	* Makefile.am: Created Makefile.am in util subdirectory

2005-01-24 06:14  twu

	* util/gmap_setup.pl.in: Fixed bug due to missing quotation mark

2005-01-24 06:14  twu

	* configure.ac: Removed dependence upon popt library

2005-01-23 15:14  twu

	* util/gmap_setup.pl.in: Added procedures for handling UCSC
	  genomes.

2005-01-23 15:13  twu

	* src/iit_store.c: Using Tableint_T instead of Table_T for types.

2005-01-23 15:13  twu

	* src/Makefile.am: Removed some unnecessary source files.

2005-01-23 15:12  twu

	* configure.ac: Added ACX_EXPAND, turned off popt, and fixed
	  problem when no threads compilation is possible.

2005-01-23 15:12  twu

	* config.site.gne: Added comments for profiling and making .third
	  file.

2005-01-23 15:11  twu

	* acinclude.m4: Added macro for ACX_EXPAND.

2005-01-23 15:11  twu

	* README: Added mention of examples and make check.

2005-01-23 15:11  twu

	* Makefile.am: Added extra dist files for examples.

2005-01-23 14:25  twu

	* src/oligoindex.c: Created a union type to make clear the possible
	  storage of either a position or a pointer to an array positions.

2005-01-23 14:24  twu

	* src/datadir.c: Removed unused function.

2005-01-23 14:23  twu

	* src/: table.c, table.h, tableint.c, tableint.h, uinttable.c,
	  uinttable.h, gmapindex.c: Added an end value to avoid problems
	  when table length is 0.

2005-01-23 12:44  twu

	* src/gmap.c: Removed duplicate getopt line.

2005-01-23 12:44  twu

	* src/iit_get.c: Fixed compilation bug when popt not available.

2005-01-23 12:43  twu

	* src/gmapindex.c: Used specific table types and keys/values
	  functions.

2005-01-23 12:43  twu

	* src/: table.c, table.h: Made functions Table_keys and
	  Table_values

2005-01-23 12:42  twu

	* src/: tableint.h, uinttable.c, uinttable.h, Makefile.am: Made
	  specific table types.

2005-01-23 12:38  twu

	* src/tableint.c: Made specific table types.

2005-01-23 09:32  twu

	* util/Makefile.am: Removed Makefile.am

2005-01-23 09:32  twu

	* util/gmap_uncompress.pl.in: Using BINDIR for substitution.

2005-01-23 05:02  twu

	* util/gmap_setup.pl.in: Major changes made to provide both
	  interactive and command-line use.

2005-01-22 04:30  twu

	* configure.ac: Allowed hyphens to be in the version number

2005-01-22 04:30  twu

	* MAINTAINER, bootstrap, config.site, config.site.gne: Added local
	  config.site to CVS directory

2005-01-22 03:56  twu

	* MAINTAINER: Added notes for maintainer

2005-01-22 03:32  twu

	* README: Simplifying the installation instructions

2005-01-22 03:04  twu

	* configure.ac: Made configuration easier by adding VERSION and
	  config.site files.  Removed MAPDIR.  Added Perl scripts.

2005-01-22 03:03  twu

	* VERSION, config.site: Made configuration easier by adding VERSION
	  and config.site files.

2005-01-22 03:02  twu

	* util/: gmap_compress.pl.in, gmap_uncompress.pl.in: Changed file
	  from .pl version to .pl.in version.

2005-01-22 03:02  twu

	* src/: datadir.c, datadir.h, gmap.c: Moved map files to a
	  subdirectory in genome directory.

2005-01-22 03:01  twu

	* src/Makefile.am, util/Makefile.am: Moved Perl scripts to util
	  subdirectory.

2005-01-22 02:11  twu

	* src/gmapsetup.pl.in: Moved file to util subdirectory.

2005-01-22 02:03  twu

	* util/whats_on: Changed location of map files to be inside genome
	  directories.

2005-01-22 02:03  twu

	* util/: gmap_compress.pl, gmap_uncompress.pl: Changing scripts
	  from .pl to .pl.in version

2005-01-21 23:38  twu

	* README, configure.ac, src/Makefile.am, src/compress.c,
	  src/datadir.c, src/genome.c, src/get-genome.c, src/gmap.c,
	  src/gmapsetup.pl.in, src/iit-read.c, src/indexdb.c,
	  src/segmentpos.c, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/gmap_setup.pl.in: Renamed program
	  from snap to gmap

2005-01-21 23:21  twu

	* util/: snap_compress.pl, snap_uncompress.pl: Renamed program from
	  snap to gmap

2005-01-21 23:16  twu

	* src/: snapindex.c, snapbuild.pl.in: Renamed program from snap to
	  gmap

2005-01-21 23:12  twu

	* src/snap.c: Renamed program from snap to gmap

2005-01-21 22:56  twu

	* util/: gmap_compress.pl, gmap_compress.pl.in, snap_compress.pl:
	  Better handling of MD5 info and aa lines.

2005-01-21 22:55  twu

	* util/: gmap_uncompress.pl, gmap_uncompress.pl.in,
	  snap_uncompress.pl: Handling arbitrary flags in compression.

2005-01-21 22:50  twu

	* src/: mutation.c, mutation.h, pair.c, pair.h, pairdef.h,
	  translation.c: Added refquerypos to print nucleotide position of
	  mutations.

2005-01-21 22:48  twu

	* src/get-genome.c: Fixed problem with empty header for reference
	  sequence when specific strain is requested.

2005-01-19 01:51  twu

	* src/translation.c: Fixed problem with printing of an AA in an
	  intron.

2005-01-19 01:50  twu

	* src/mutation.c: Consolidated point mutations near a segmental
	  mutation.

2005-01-06 01:22  twu

	* src/translation.c: Fixed detection of deletion mutations where
	  aapos was advancing in a gap.

2005-01-06 01:15  twu

	* src/: translation.c, mutation.c, mutation.h: Fixed cases where a
	  single-position mutation was reported next to a segmental
	  mutation.

2005-01-06 01:15  twu

	* src/stage3.c: Added debugging statements for relative alignment.

2005-01-05 09:27  twu

	* src/translation.c: Allowed lower case letters to translate
	  appropriately to a codon.

2004-12-21 05:25  twu

	* src/stage3.c: Performing microexon search for all defect rates.
	  Adjusted acceptable mismatches for low-quality sequences.

2004-12-20 09:04  twu

	* src/translation.c: Increased IGNORE_MARGIN to deal with
	  nucleotide coordinates.

2004-12-20 09:04  twu

	* src/stage3.c: Changed criteria for performing microexon search.

2004-12-20 03:28  twu

	* src/: translation.c, translation.h: Fixed detection of large
	  deletions relative to reference sequence.  Fixed printing of cDNA
	  aa in a gap.

2004-12-20 03:27  twu

	* src/stage3.c: Changed criterion for starting microexon search to
	  add mismatches and indels.  Fixed detection of large deletions
	  relative to reference sequence.

2004-12-20 03:26  twu

	* src/: gmap.c, snap.c: Set chimera threshold to 0 for default.
	  Reduced band from 10 to 7.

2004-12-20 03:25  twu

	* src/dynprog.c: Reduced pvalue thresholds for microexons.

2004-12-19 02:19  twu

	* src/: gmap.c, snap.c: Turned on chimera functionality.  Increased
	  dynamic programming band from 7 to 10.

2004-12-19 02:18  twu

	* src/stage1.c: Changed function for maxintronlen.

2004-12-19 02:17  twu

	* src/smooth.c: Increased SHORTMIDEXON_LEN from 40 to 80.

2004-12-19 02:17  twu

	* src/dynprog.c: Removed definition for INFINITY, which wasn't
	  being used.

2004-12-18 03:12  twu

	* src/stage2.c: Created define parameter SAMPLE_INTERVAL.

2004-12-18 03:12  twu

	* src/: gmap.c, snap.c: Change maxintronlen to be
	  maxintronlen_bound, and compute new maxintronlen depending on
	  current query length.  Increased size of extraband_single and
	  extraband_paired.

2004-12-18 03:10  twu

	* src/: params.c, params.h, stage1.c, stage1.h: Change maxintronlen
	  to be maxintronlen_bound, and compute new maxintronlen depending
	  on current query length.

2004-12-18 03:05  twu

	* src/dynprog.c: Changed compute_scores_affine to have parameter
	  list compatible with compute_scores (with codon penalty).

2004-12-17 22:43  twu

	* src/stage3.c: Subtracting points for non-canonical introns in
	  determining direction.  Doing middle introns of sequence before
	  doing 3' and 5' ends.

2004-12-17 22:42  twu

	* src/dynprog.c: Increased pvalue thresholds.

2004-12-13 03:06  twu

	* src/stage3.h: Added function for printing cDNA exons.

2004-12-13 03:06  twu

	* src/stage3.c: Fixed problem where we shouldn't perform single-gap
	  dynamic programming because unable to peel forward and peel back.

2004-12-13 03:03  twu

	* src/: pair.c, pair.h, gmap.c, snap.c: Added function for printing
	  cDNA exons.

2004-12-13 03:02  twu

	* src/translation.c: Created separate mutation types for
	  substitution, insertion, and deletion.  Allowed filling in of
	  last amino acid.

2004-12-13 03:02  twu

	* src/: mutation.c, mutation.h: Created separate mutation types for
	  substitution, insertion, and deletion.

2004-12-09 11:34  twu

	* src/stage3.c: Changed calls to Translate module.

2004-12-09 11:34  twu

	* src/translation.c: Simplified code for computing protein bounds.
	  Handled the case where full length is specified, but no full
	  length protein exists.

2004-12-09 11:32  twu

	* src/: mutation.c, mutation.h: Added procedures for handling
	  multiple insertions and deletions.

2004-12-09 01:33  twu

	* src/: translation.c, translation.h: Changed algorithm for
	  translate_est_forward and translate_est_backward.

2004-12-08 03:14  twu

	* src/: translation.c, translation.h: Changed algorithms for
	  translate_est_forward and translation_est_backward.  Added
	  printing of nucleotide differences.

2004-12-08 03:12  twu

	* src/: gmap.c, snap.c, stage3.c, stage3.h: Added options for
	  printing either genomic or cDNA version of protein.

2004-12-08 03:11  twu

	* src/: pair.c, pair.h: Added function Pair_dump_aapos.

2004-12-08 03:11  twu

	* src/: mutation.c, mutation.h: Added functions for retrieving
	  amino acids from mutation.

2004-12-08 03:10  twu

	* src/dynprog.c: Added slight penalty against gaps next to an
	  intron.

2004-12-05 13:50  twu

	* src/: pair.c, pair.h, pairdef.h, pairpool.c: Now printing both
	  genomic and cDNA proteins.

2004-12-05 13:49  twu

	* src/: translation.c, translation.h, mutation.c, mutation.h,
	  Makefile.am, stage3.c: Simplified computation of translations and
	  mutations.

2004-12-02 01:48  twu

	* src/stage3.h: Removed unused chimera code.

2004-12-02 01:48  twu

	* src/stage3.c: Removed unused chimera code.  Changed criteria for
	  finding microexons at end; now performed only when extension is
	  poor and sequence quality is high.

2004-12-02 01:46  twu

	* src/: dynprog.h, gmap.c, snap.c: Allowed user option to extend
	  alignment past last match.

2004-12-02 01:46  twu

	* src/dynprog.c: Fixed bug in adding gap to replace dashes.

2004-12-02 01:45  twu

	* src/pairpool.c: Added debugging statement for creation of pairs.

2004-12-02 01:45  twu

	* src/smooth.c: Added check for negative exon length.

2004-11-29 09:09  twu

	* src/: dynprog.c, dynprog.h: Added symbols for an intron if
	  applicable to a large horizontal jump.  Increased maximum
	  microexon size.

2004-11-29 09:07  twu

	* src/stage3.c: Added peel_back and peel_forward to 5' and 3' ends
	  before doing search for microexons.

2004-11-22 08:25  twu

	* src/: stage1.c, stage1.h: Removed unused code.

2004-11-22 08:25  twu

	* src/: scores.h, stage3.c: Added credit for dual half-canonical
	  introns.

2004-11-22 08:25  twu

	* src/dynprog.c: Added parameters for PVALUE for microexon and end
	  exon searches.

2004-11-18 02:21  twu

	* src/result.h: Changed interface for Result_new to match
	  implementation.

2004-11-18 02:20  twu

	* src/Makefile.am: Added scores.h to Makefile.am.

2004-11-15 01:16  twu

	* src/: stage3.c, stage3.h: Commented out code for extending pairs
	  in a chimera.

2004-11-15 01:16  twu

	* src/: gmap.c, snap.c: Fixed problem in rearranging best two paths
	  for chimera.

2004-11-15 01:14  twu

	* src/pair.c: Stopped printing of the terminal amino acid '*'.

2004-11-15 01:12  twu

	* src/: genome.c, indexdb.c: Added printing of a dot every 10000
	  pages.

2004-10-12 08:20  twu

	* src/: gmap.c, snap.c: For chimeras that extend too long, now
	  chopping off the extra part.

2004-10-12 08:20  twu

	* src/: stage3.c, stage3.h: Added procedure for doing a bounded
	  copy of a Stage 3 object.

2004-10-12 08:19  twu

	* src/: pairpool.c, pairpool.h: Added procedure for doing a bounded
	  copy of a path.

2004-10-06 10:13  twu

	* src/scores.h: Moved scores for determining goodness into a
	  separate file.

2004-10-06 10:12  twu

	* src/: gmap.c, snap.c, chimera.c, chimera.h, Makefile.am: Changed
	  procedure for chimeras to find best pair and to order the
	  chimeras according to query sequence.

2004-10-06 10:10  twu

	* src/: stage3.c, stage3.h: Added procedure for copying a Stage3
	  object.

2004-10-06 10:09  twu

	* src/: result.c, result.h: Changed chimera information to be a
	  position, rather than a boolean.

2004-10-06 10:06  twu

	* src/dynprog.c: Added code for allowing right angles, but not
	  using at present.

2004-10-06 10:05  twu

	* src/pairpool.c: Changed print statement to work only in debug
	  mode.

2004-10-06 10:05  twu

	* src/: pair.c, pair.h: Added procedure for computing scores along
	  a path.

2004-09-30 10:39  twu

	* src/: match.c, pair.c, gmap.c, pair.h, sequence.c, sequence.h,
	  snap.c, stage3.c, stage3.h: Added MD5 checksum for compressed
	  output.

2004-09-30 10:39  twu

	* src/stage1.c: Added notation about using position for revcomp
	  matches in IITs.

2004-09-30 10:38  twu

	* src/iit-read.c: Changed debugging statements to print unsigned
	  ints.

2004-09-27 08:50  twu

	* src/stage3.c: Fixed problem when peeling an extra pair if it's a
	  gap.

2004-09-09 08:46  twu

	* src/stage3.c: Restored behavior of crossing just one short exon
	  for dual genome gap.

2004-09-09 08:40  twu

	* src/stage3.c: Peeled back one more matching pair.  For dual
	  intron gap, now skipping multiple short exons and keeping the
	  longest one.

2004-09-09 08:38  twu

	* src/: gmap.c, snap.c: Increased maxpeelback from 10 to 11.

2004-09-09 08:38  twu

	* src/: pairpool.c, pairpool.h: Added command
	  Pairpool_transfer_copy, although not currently used.

2004-09-09 08:37  twu

	* src/: pair.c, pair.h: Added command Pair_check_list.

2004-09-09 08:37  twu

	* src/dynprog.c: Added end reward for bridging a cDNA gap.

2004-09-09 08:35  twu

	* src/md5-compute.c: Changed behavior from a single sequence to a
	  FASTA file of multip[le sequences.

2004-09-09 08:35  twu

	* src/Makefile.am: Added object file for md5-compute.

2004-09-02 07:36  twu

	* src/stage3.c: Fixed floating exception bug when middle_exonlength
	  is non-positive.

2004-09-02 07:35  twu

	* src/stage2.c: Fixed problem of reading uninitialized value.

2004-08-30 03:05  twu

	* src/dynprog.c: Added check for non-positive span.

2004-07-28 06:05  twu

	* src/stage2.c: Changed some penalties.  Using bad sequence
	  information to increase lookback.

2004-07-28 06:04  twu

	* src/: oligoindex.c, oligoindex.h: Added check for bad sequences
	  (with several non-ACGTN characters).

2004-07-28 06:03  twu

	* src/dynprog.c: Added check for zero span.

2004-06-25 03:59  twu

	* src/: gmap.c, snap.c: Added flag to search only reference strain.

2004-06-25 03:59  twu

	* src/stage2.c: Increased definition of ENOUGH_CONSECUTIVE.  Added
	  penalties for deadp.

2004-06-25 03:58  twu

	* src/stage3.c: Penalizing noncanonical introns in comparing across
	  different paths.

2004-06-25 03:56  twu

	* src/segmentpos.c: Changed output of contig length.

2004-06-25 03:56  twu

	* src/: pair.c, pair.h: Reporting number of noncanonical introns.
	  Allowing goodness to be reported during debugging.

2004-06-20 00:02  twu

	* src/stage2.c: Simplified decision making for mismatch gaps.
	  Increased penalties on gendistance and querydistance.

2004-06-16 08:24  twu

	* util/whats_on: Added get_sequences function.

2004-06-16 08:23  twu

	* util/: gmap_uncompress.pl, gmap_uncompress.pl.in,
	  snap_uncompress.pl: Implemented code to interpret new compression
	  scheme.

2004-06-16 08:22  twu

	* src/stage2.c: Changed penalty functions into macros for speed.
	  Made some other changes to improve speed.

2004-06-16 08:21  twu

	* src/dynprog.c: Fixed bug involving uninitialized variable.

2004-06-15 07:51  twu

	* src/stage2.c: Penalizing intron length per 2000 nt instead of
	  1000.

2004-06-15 07:50  twu

	* src/stage3.c: Using goodness scores to decide between single and
	  dual introns.  Searching for microexons only when sequence
	  quality is medium to high.

2004-06-15 07:49  twu

	* src/: dynprog.c, dynprog.h: Reporting nopens and nindels from
	  Dynprog_genome_gap.

2004-06-12 12:27  twu

	* src/stage3.c: Added evaluation of middle exon length in deciding
	  between single and dual introns.

2004-06-12 12:27  twu

	* src/stage2.c: Reduced size of INTRON_DEFN.  Further penalized
	  large query distances.

2004-06-12 12:26  twu

	* src/stage1.c: Increased length of additional ends of genome
	  segment.

2004-06-12 12:26  twu

	* src/oligoindex.c: Improved debugging statements.

2004-06-12 12:25  twu

	* src/: dynprog.c, dynprog.h: Allowing up to 1 mismatch on either
	  side for microexon search.  Reporting position of exonhead in
	  Dynprog_genome_gap for use in traversing dual genome gap.

2004-06-10 03:27  twu

	* src/stage2.c: Added procedure to determine maximum intron length
	  at a given querypos, and based penalties to be linear with that.

2004-06-10 03:26  twu

	* src/smooth.c: Added check for nullness of intronlengths.

2004-06-10 03:26  twu

	* src/dynprog.c: Added probabilistic check on microexon length for
	  a given genomic span.

2004-06-09 09:22  twu

	* src/: pair.c, pair.h, stage3.c: Keeping track of semicanonical
	  introns and scoring them to decide on strand.

2004-06-09 09:19  twu

	* src/smooth.c: Made decision about deleting end exons based on
	  probability.

2004-06-08 06:32  twu

	* src/get-genome.c: Fixed a bug in determining whether a query is a
	  range.

2004-06-07 10:37  twu

	* src/stage3.c: Added debugging statement for microexons.

2004-06-07 10:37  twu

	* src/dynprog.c: Added minimum length for introns when looking for
	  microexons.

2004-06-07 09:29  twu

	* src/stage2.c: Changed penalties to be more consistent on
	  mismatches between different conditions, including deadp.  For
	  deadp, now requiring that abs(gendistance - querydistance) or
	  querydistance be less than INTRON_DEFN.

2004-06-07 09:27  twu

	* src/smooth.c: Increased threshold on ends to be 20.

2004-06-07 09:27  twu

	* src/pair.c: For determining fracidentity (and selecting between
	  forward and reverse strands), now counting semicanonical introns
	  as canonical.

2004-06-07 05:12  twu

	* src/stage2.c: For deadp, increased lookback.

2004-06-07 04:57  twu

	* src/: gmap.c, snap.c: Increased maxintronlen from 1 million bp to
	  2 million bp.  Motivated by HER4 (NM_005235).

2004-06-07 04:55  twu

	* src/: gmap.c, snap.c: Increased nullgap from 80 to 600.

2004-06-07 04:55  twu

	* src/stage2.c: Modified stage 2 scoring for mismatch alignments.
	  Invoked deadp when fwd or rev score is zero.

2004-06-04 06:33  twu

	* src/translation.c: Further fixed the bug involving uninitialized
	  heap (translation_start/translation_end extending beyond sequence
	  boundaries).

2004-06-04 03:56  twu

	* src/: stage2.c, stage2.h: Rewrote code into separate procedure.
	  Increased gendistance penalty.  Changed penalties when querypos
	  is dead.

2004-06-04 03:55  twu

	* src/: gmap.c, snap.c: Created separate parameters for
	  extraband_end and extraband_paired.  Renamed maxlookback to
	  nullgap.  Created nsufflookback parameter.  Removed repetition of
	  stage 2.

2004-06-04 03:53  twu

	* src/: params.c, params.h, stage3.c, stage3.h: Created separate
	  parameters for extraband_end and extraband_paired.  Renamed
	  maxlookback to nullgap.  Created nsufflookback parameter.

2004-06-04 03:53  twu

	* src/dynprog.h: Created separate parameters for extraband_end and
	  extraband_paired.

2004-06-04 03:53  twu

	* src/dynprog.c: Created separate parameters for extraband_end and
	  extraband_paired.  Extending last nucleotide at ends if possible.
	  Removing gaps at ends.

2004-06-04 03:52  twu

	* src/translation.c: Fixed a bug involving reading/writing of
	  uninitialized heap.

2004-06-02 09:08  twu

	* src/stage3.c: Doubled intron space required for a paired gap
	  solution to be attempted.

2004-06-02 09:07  twu

	* src/dynprog.c: Implemented gap penalties that are non-affine,
	  with extensions being the same within a codon.

2004-06-02 07:17  twu

	* src/translation.c: Fixed bug where codon was assigned improperly
	  at a cDNA gap.

2004-06-02 00:16  twu

	* src/: stage3.c, dynprog.c, dynprog.h: Added a conservative search
	  for microexons at the 5' and 3' ends.

2004-06-02 00:15  twu

	* src/smooth.c: Increased pruning of ends from 8 back to 16.

2004-06-01 12:12  twu

	* src/: stage2.c, stage2.h: Added Stage2_pathlength function.

2004-06-01 12:12  twu

	* src/: gmap.c, snap.c: ncreased maxpeelback from 8 to 10 and
	  allowed program to redo stage2 with increased suflookback if cDNA
	  not covered.

2004-06-01 12:11  twu

	* src/stage3.h: Changed MININTRONLEN from 9 to 6 and moved
	  definition into .c file.

2004-06-01 12:05  twu

	* src/stage3.c: Made search for microexon dependent on number of
	  mismatches.

2004-06-01 12:03  twu

	* src/: dynprog.c, dynprog.h: Made Dynprog_genome_gap return number
	  of matches and mismatches.

2004-05-26 10:39  twu

	* src/: dynprog.c, dynprog.h, stage3.c: Made microexon search work
	  in reverse direction.  Fixed memory leak.

2004-05-26 10:38  twu

	* src/boyer-moore.h: Added RCS Id.

2004-05-26 10:38  twu

	* src/boyer-moore.c: Removed debugging statement.  Added RCS Id.

2004-05-26 10:23  twu

	* src/: Makefile.am, boyer-moore.c, boyer-moore.h, dynprog.c,
	  dynprog.h, stage3.c: Added procedure for finding microexons.
	  Works for forward direction only.

2004-05-26 07:26  twu

	* src/stage3.c: Increased goodness score for canonical intron when
	  deciding between forward and reverse directions.

2004-05-26 04:30  twu

	* src/sequence.c: Fixed read procedure to handle PC line feeds.

2004-05-26 04:30  twu

	* src/dynprog.c: Changed end extension to allow one gap and to
	  proceed if number of matches is greater than or equal to number
	  of mismatches.

2004-05-26 02:24  twu

	* src/: gmap.c, snap.c, stage3.c, stage3.h, translation.c,
	  translation.h: Added option for assuming a full-length sequence.

2004-05-26 02:23  twu

	* src/pair.c: Changed printing of protein coordinates to correspond
	  to first amino acid on each line.

2004-05-26 02:02  twu

	* src/: gmap.c, snap.c: Added ability to print protein sequence.
	  Fixed some flags.

2004-05-26 01:55  twu

	* src/: translation.c, translation.h: Fixed calculation of
	  translation coordinates.

2004-05-26 01:53  twu

	* src/: pair.c, pair.h, stage3.c, stage3.h: Added printing of
	  protein coordinates.

2004-05-26 01:52  twu

	* src/indexdb.c: Revised monitoring statement.

2004-05-26 01:51  twu

	* src/dynprog.c: Revised extensions of 5' and 3' ends to use best
	  score with no gap, even if negative.	This extends ends when
	  there is one match and one mismatch.

2004-05-05 10:00  twu

	* src/: compress.c, indexdb.c, pair.c, gmap.c, snap.c, stage3.c,
	  stage3.h, translation.c, translation.h: Made improvements to
	  relative translation routines.

2004-05-05 09:54  twu

	* src/: Makefile.am, compress.c, compress.h, gmapindex.c,
	  indexdb.c, snapindex.c: Moved compress and uncompress routines to
	  a new file.

2004-04-22 10:03  twu

	* src/translation.c: Fixed frameshift-tolerant protein computation
	  for cases where cDNA deletion is 3 or more nt.

2004-04-22 07:02  twu

	* src/: gmap.c, snap.c, stage3.c, stage3.h, translation.c,
	  translation.h: Added feature for fixing frameshifts in
	  reference-based protein computation and made it the default.

2004-04-22 03:58  twu

	* src/: stage3.c, translation.c, translation.h: Changed internal
	  data format for calculating translations.

2004-04-21 23:53  twu

	* src/translation.c: Fixed array bounds bug in translating from
	  reference.

2004-04-21 17:20  twu

	* util/whats_on: Added flag for showing original headers.

2004-04-21 11:09  twu

	* src/: pair.c, pair.h, pairdef.h, pairpool.c, params.c, gmap.c,
	  params.h, snap.c, stage3.c, stage3.h, translation.c,
	  translation.h: Added protein calculation for ESTs based on a
	  reference mRNA.

2004-04-18 23:15  twu

	* src/: gmap.c, pair.c, pair.h, params.c, params.h, snap.c,
	  stage3.c, stage3.h, translation.c, translation.h: Changes to
	  allow calculation of mutation effect given a specific mutation

2004-04-18 04:56  twu

	* src/: genome.c, genome.h: Fixed code for patching strains.

2004-04-18 04:55  twu

	* src/genomicpos.c: Cleaned up code for adding commas.

2004-04-18 04:55  twu

	* src/stage1.c: Changed variable name from stutter to stutterdist.

2004-04-18 04:54  twu

	* src/: gmap.c, snap.c: Added internal flag to control strain
	  searching feature.

2004-04-17 00:53  twu

	* util/whats_on: Added ability to print align.iit files, rather
	  than map.iit files.

2004-04-17 00:10  twu

	* util/: gmap_uncompress.pl, gmap_uncompress.pl.in,
	  snap_uncompress.pl: Added inversion mode.

2004-04-17 00:10  twu

	* util/: gmap_compress.pl, gmap_compress.pl.in, snap_compress.pl:
	  Added code to skip protein sequence lines.

2004-03-30 04:10  twu

	* src/: gmap.c, snap.c, Makefile.am: Added routines for printing
	  protein sequence.

2004-03-30 04:09  twu

	* src/: iit-read.c, iit-read.h: Added procedure for listing all
	  types.

2004-03-30 04:07  twu

	* src/: stage3.c, stage3.h: Fixed memory leak and bug when stage3
	  result is NULL.

2004-03-30 04:06  twu

	* src/: translation.c, translation.h: Added routines for printing
	  peptide sequence.

2004-03-30 04:06  twu

	* src/get-genome.c: Allowed user to select a particular strain to
	  align against.

2004-03-30 04:05  twu

	* src/: pair.c, pair.h: Added routine for printing peptide.
	  Clarified code for handling inversions on minus strand.  Fixed
	  bug in compression for '#' character.

2004-02-23 09:50  twu

	* src/stage3.c: Added special cases for single mismatch and single
	  cDNA insertion.

2004-02-23 09:50  twu

	* src/stage1.c: Defined maximum on finding match pairs, to
	  eliminate slow response on nonsense sequences, such as poly-G.

2004-02-23 00:22  twu

	* src/stage3.c: In pass 3, force single gap to be crossed even if
	  finalscore is negative, to complete alignment.

2004-02-18 16:45  twu

	* src/: stage3.c, stage3.h: Removed unused variable minendtrigger.

2004-02-18 16:44  twu

	* src/: params.c, params.h, gmap.c, snap.c: Removed global
	  user-specified parameters from Params_T.

2004-02-18 16:02  twu

	* src/: gmap.c, snap.c: Removed fraction_threshold parameter.
	  Changed default chimera_threshold to 0.50.

2004-02-18 16:02  twu

	* src/: params.c, params.h: Removed fraction_threshold parameter.

2004-02-18 13:07  twu

	* src/: gmap.c, snap.c: Made chimera threshold definable by user,
	  and set default to 0.70.

2004-02-18 13:07  twu

	* src/stage3.c: Re-defined criterion for a gap to be when queryjump
	  <= 0 and genomejump <= 0, which holds true after single gaps are
	  filled.  Prevented filling in a genome gap when its alignment
	  score is negative.

2004-02-18 13:06  twu

	* src/: smooth.c, smooth.h: Re-defined criterion for a gap to be
	  when queryjump <= 0 and genomejump <= 0, which holds true after
	  single gaps are filled.

2004-02-18 08:48  twu

	* src/: matchpair.c, matchpair.h: Made size bound a fraction of the
	  best, rather than subtraction.

2004-02-18 08:48  twu

	* src/stage1.c: Increased maxentries parameters.  Made size bound a
	  fraction of the best, rather than subtraction.

2004-02-18 08:47  twu

	* src/: gmap.c, snap.c: Removed calls to Stage1_matchpairlist.	Now
	  performing sampling by default.

2004-02-18 08:46  twu

	* src/smooth.c: Reduced size definition of short intron.  Made
	  intron definition depend only on genome distance, which now
	  includes single gaps that weren't filled in in stage 3.

2004-02-18 08:45  twu

	* src/stage2.c: Made a macro for query distance penalty.

2004-02-18 08:45  twu

	* src/stage3.c: Fixed problem with peeled is NULL.  Added decision
	  to not fill in single gap if the score is negative, and to
	  restore peeled pairs in that case.

2004-02-17 22:26  twu

	* src/smooth.c: Fixed memory leak.

2004-02-17 09:30  twu

	* src/stage3.c: Fixed bug where program would skip over a pair
	  after gappairs was added.

2004-02-16 18:24  twu

	* src/stage3.c: Made peel_back and peel_forward end at a non-gap,
	  by backtracking from peeled.

2004-02-16 10:02  twu

	* src/stage3.c: Increased reward for canonical introns from 5 to 8.

2004-02-15 15:20  twu

	* src/stage3.c: Fixed bugs in peel_back and peel_forward.  Fixed
	  bug in computing goodness scores.

2004-02-15 02:10  twu

	* src/: smooth.c, smooth.h, stage3.c: Giving information about
	  number of short exons found in smoothing to stage 3 to help
	  improve speed.

2004-02-15 01:17  twu

	* src/stage3.c: Removed occurrences of indexsize.  Cleaned up
	  procedure for finding middle exons in dual intron procedure.

2004-02-15 01:15  twu

	* src/: smooth.c, smooth.h: Rewrote smoothing procedure to be a
	  cleaner procedure.  Analyzing both ends to prune short exons.

2004-02-15 01:14  twu

	* src/: pair.c, pair.h: Added Pair_debug_alignment procedure.

2004-02-14 13:09  twu

	* src/: stage3.c, smooth.c, smooth.h, stage2.c: Changed stage 2 to
	  produce a nucleotide-based path, rather than 8-mer path.  Changed
	  smoothing and stage 3 accordingly.  Made all intron distance
	  penalties equal in stage 2.

2004-02-14 01:58  twu

	* src/: dynprog.c, dynprog.h, stage3.c: Rearranged stage 3 to solve
	  dual introns before other introns and large gaps.  Performing
	  smoothing iteratively with dual introns.

2004-02-14 01:57  twu

	* src/stage2.c: Replaced calculations of gendistance_penalty with
	  macros.

2004-02-14 01:08  twu

	* src/smooth.c: Increased minexonlen for smoothing, because
	  smoothing has been made iterative.

2004-02-14 01:07  twu

	* src/pair.c: Using memcpy commands instead of copying individual
	  fields.  Added diagnostic printing of short exons.

2004-02-13 22:12  twu

	* src/matchpair.c: Fixed memory leak.

2004-02-13 22:12  twu

	* src/: smooth.c, smooth.h, stage3.c, Makefile.am: Added files
	  smooth.c and smooth.h and moved Smooth_path there

2004-02-13 10:52  twu

	* src/: gmap.c, snap.c, stage2.c, stage2.h, stage3.c, stage3.h:
	  Changed stage 2 and stage 3 algorithms to interleave in the
	  following order: dynamic programming on single gaps, then
	  smoothing, then dynamic programming on ends and large gaps.
	  Allows dual intron algorithm to work even when middle exon has
	  small mismatches or gaps.

2004-02-13 10:45  twu

	* src/pair.c: Fixed merge_one_gap to handle user-selected ngap !=
	  3.

2004-02-13 10:45  twu

	* src/: dynprog.c, dynprog.h: Moved definitions of defect rate
	  boundaries to header file.

2004-02-13 07:58  twu

	* src/stage2.c: Subtracting (querydistance+7)/8 on mismatches to
	  penalize once per 8-mer.  Subtracting 1 for each intron to reduce
	  number of introns, especially when a/1000 + b/1000 < (a+b)/1000.

2004-02-13 05:16  twu

	* src/stage2.c: Added separate intron penalties for consistent,
	  unknown, and inconsistent introns.  Increased lengths of short
	  middle exons marked for dual genome gap.

2004-02-13 02:54  twu

	* src/stage2.c: Implemented two parallel computations in Stage 2
	  under forward and reverse assumptions.  Removed firstregion and
	  lastregion computations from smoothing.

2004-02-13 02:52  twu

	* src/: stage3.c, stage2.h: Added intron length to goodness score.

2004-02-11 22:55  twu

	* src/: gmap.c, snap.c: Removed universalp flag (-U).

2004-02-11 22:54  twu

	* src/iit_get.c: Added annotation only mode (-A).

2004-02-11 08:11  twu

	* util/whats_on: Simplified code greatly.

2004-02-11 08:11  twu

	* util/: gmap_compress.pl, gmap_compress.pl.in, snap_compress.pl:
	  Removed space before first token.  Fixed bug in reporting genomic
	  exon length rather than cDNA exon length.

2004-02-11 06:53  twu

	* src/: dynprog.c, dynprog.h, stage3.c: Added computation of
	  nonintronlen for goodness ranking.

2004-02-11 05:15  twu

	* src/stage2.c: Introduced Link_T to hold dynamic programming data.

2004-02-11 04:22  twu

	* src/stage2.c: Modified smoothing to have keep, delete, and mark
	  options.

2004-02-11 03:29  twu

	* src/: stage2.c, stage2.h, stage3.c: Added category for introns of
	  unknown direction.

2004-02-11 03:28  twu

	* src/: gmap.c, snap.c: Made default for chimerasearchp false
	  again.  Added an automatic mode for chimera search if coverage is
	  less than 50%.

2004-02-10 10:57  twu

	* src/: gmap.c, snap.c: Made chimera search the default.

2004-02-10 10:57  twu

	* src/stage2.c: Added counts of forward, reverse, and non-canonical
	  introns to the dynamic programming procedure, and used
	  consistency in computing scores.

2004-02-10 03:27  twu

	* src/stage3.c: Added debugging macros.

2004-02-10 03:27  twu

	* src/stage2.c: Added intron penalty only for noncanonical introns.

2004-02-10 03:25  twu

	* src/stage1.c: Added debugging statements.

2004-02-10 03:25  twu

	* src/matchpair.c: Reduced MAXCANDIDATES from 30 to 10.

2004-02-10 03:25  twu

	* src/: dynprog.c, pair.c, pairdef.h: Added '~' character for
	  non-canonical gaps converted to insertions, to avoid penalizing
	  them as non-intron gaps.

2004-02-09 13:07  twu

	* src/: iit-read.c, iit-read.h, gmap.c, snap.c, stage3.c, stage3.h:
	  Changed map output to include strand if both strands are
	  requested.

2004-02-09 13:07  twu

	* src/dynprog.c: Restored horizontal or vertical jump of 1 next to
	  intron.

2004-02-09 13:06  twu

	* src/datadir.c: Changed error message.

2004-02-09 13:06  twu

	* src/stage2.c: Add penalty for number of non-canonical introns.
	  Accumulate best score for introns, even if negative, and use that
	  if no other score exceeds 0.

2004-02-09 02:02  twu

	* src/iit-read.h: Added name to IIT structure.

2004-02-09 01:53  twu

	* src/stage3.c: Added compression feature.  Added debug mode to
	  show output from stage 2.

2004-02-09 01:52  twu

	* src/: gmapindex.c, snapindex.c: Added optional name to IIT
	  structure.

2004-02-09 01:52  twu

	* src/: pair.c, pair.h, params.c, params.h, gmap.c, snap.c,
	  stage3.h: Added compression feature.

2004-02-09 01:46  twu

	* src/: iitdef.h, get-genome.c, iit-read.c, iit_dump.c, iit_get.c:
	  Added optional name to IIT structure.

2004-02-06 15:00  twu

	* src/dynprog.c: Advanced counter within gaps to the next position.

2004-02-06 14:39  twu

	* src/: pair.c, pair.h, pairdef.h, pairpool.c: Added the shortexonp
	  field for pairs.

2004-02-06 14:38  twu

	* src/stage2.c: For smoothing of short exons, marking positions as
	  short, rather than deleting them.  Increased length threshold for
	  short exons, because we now have a mechanism for handling them
	  well.

2004-02-06 14:37  twu

	* src/: gmap.c, snap.c: Added a dynprogM for handling short exons.

2004-02-06 14:36  twu

	* src/: stage3.c, stage3.h: Removed special procedure for dual
	  genome gaps.	Instead comparing a single genome gap with two half
	  genome gaps for short exons.

2004-02-06 14:33  twu

	* src/dynprog.c: Removed special procedure for dual genome gaps.
	  Instead, for short exons, comparing a single genome gap with two
	  half genome gaps.

2004-02-06 05:26  twu

	* src/dynprog.c: Passing pointers to revsequence and revoffset from
	  stage3 to dynprog procedures where appropriate.  Added
	  preliminary code for dual genome gap.

2004-02-06 05:25  twu

	* src/: stage3.c, dynprog.h: Passing pointers to revsequence and
	  revoffset from stage3 to dynprog procedures where appropriate.

2004-02-06 03:12  twu

	* src/: get-genome.c, gmap.c, pair.c, pair.h, params.c, params.h,
	  sequence.c, sequence.h, snap.c, stage3.c, stage3.h: Added option
	  for specifying wrap length.

2004-02-06 03:10  twu

	* src/dynprog.c: Fixed problem with sequence being short by 1 nt in
	  conversion of gap to insertion.

2004-02-06 02:12  twu

	* src/dynprog.c: Convert short non-canonical introns into
	  insertions.

2004-02-06 02:03  twu

	* src/dynprog.c: Removed reverse_sequence and creation of reverse
	  sequence.  Now using a boolean to determine whether to use
	  negative indices.

2004-02-05 08:37  twu

	* README, configure.ac, src/Makefile.am, src/datadir.c,
	  src/datadir.h, src/gmap.c, src/params.c, src/params.h,
	  src/snap.c, src/stage3.c, src/stage3.h: Changed references to
	  "bounds" to "map".

2004-02-05 08:36  twu

	* util/ddsgap2_compress.pl: Made much faster.

2004-02-05 08:21  twu

	* src/get-genome.c: Fixed get-genome for reverse complement.  Added
	  debugging statements.

2004-02-05 08:20  twu

	* src/dynprog.c: Added specific constraints on whether to allow
	  gaps adjacent to the intron, depending on sequence quality.

2004-02-03 05:00  twu

	* src/: dynprog.c, dynprog.h: Removed conservative option.  Added
	  comments to explain rationale behing scoring scheme.

2004-02-03 04:58  twu

	* src/: gmap.c, snap.c, stage3.c, stage3.h, params.c, params.h:
	  Removed conservative option.

2004-02-03 02:41  twu

	* src/stage3.c: Removed peelback on sequence ends.  Continued
	  peelback through small gaps and mismatches.  Included comp of '-'
	  in pruning of gaps at end.

2004-02-03 02:40  twu

	* src/iit-read.c: Added debugging code.

2004-02-03 02:40  twu

	* src/genome.c: Fixed faulty reasoning when patch has expansion or
	  contraction.

2004-02-03 02:39  twu

	* src/dynprog.c: Raised penalties on paired gap alignment to
	  prevent gap-match-gap being preferred to two mismatches.  Added
	  checks to bridging across introns to prevent genomic insertion or
	  more than one cDNA insertion.

2004-02-02 05:31  twu

	* src/pairdef.h: Revised comment about definition of gapp.

2004-02-02 05:30  twu

	* src/: pair.c: Removed comment.

2004-02-02 05:30  twu

	* src/dynprog.c: Fixed debugging statements for pairs pushed on
	  horizontal or vertical moves.

2004-02-02 03:35  twu

	* src/: gmap.c, snap.c, pair.c, pair.h, stage3.c, stage3.h: Added
	  printing of bounds information as a separate section.

2004-01-31 10:28  twu

	* src/Makefile.am: Added uintlist.c and uintlist.h to source lists
	  where necessary.

2004-01-31 10:28  twu

	* src/: gmapindex.c, snapindex.c: Made contig intervals inclusive.

2004-01-31 10:27  twu

	* src/iit_get.c: Changed isnumber to isnumberp to avoid conflict on
	  some Unix machines.

2004-01-31 10:27  twu

	* src/iit_get.c: Handle case where strlen of annotation is 0.  Add
	  carriage return after annotation if necessary.  If one numeric
	  argument given, try as a label, then as a number.

2004-01-31 10:26  twu

	* src/iit-read.c: Handle case where strlen of annotation is 0.

2004-01-31 09:31  twu

	* src/: genome.c, get-genome.c: Reverted to previous IIT format,
	  where we don't store lengths explicitly.  For sequences, can
	  determine actual length from annotation strlen.

2004-01-31 09:30  twu

	* src/iit_dump.c: Added warning if IIT_read fails.

2004-01-31 09:29  twu

	* src/: interval.c, interval.h, iit-write.c, iit-write.h,
	  iit-read.c, iit-read.h, iit_store.c: Reverted to previous format,
	  where we don't store lengths explicitly.

2004-01-31 09:28  twu

	* src/: gmapindex.c, snapindex.c: Reverted to previous format,
	  where we don't store lengths explicitly.  For FASTA files, count
	  sequence length and store as annotation in contig_iit.

2004-01-31 09:28  twu

	* src/stage3.c: Added Pair_check procedure.

2004-01-31 04:34  twu

	* src/dynprog.c: Fixed problem with dynamic programming not going
	  back to beginning.  Fixed bridging across cDNA gaps.

2004-01-31 04:32  twu

	* src/: datadir.c, datadir.h: Created two data directories, one for
	  genome files and one for bounds files.

2004-01-31 04:31  twu

	* src/: pair.c, pair.h: Added Pair_check function.

2004-01-31 04:31  twu

	* configure.ac, src/Makefile.am, src/gmap.c, src/snap.c: Created
	  two data directories, one for genome files and one for batch
	  files.

2004-01-27 09:05  twu

	* src/dynprog.c: Reduced mismatch and gap penalties at ends to
	  extend ends more completely.

2004-01-27 01:32  twu

	* src/stage1.c: Increased length of very small sequences from 30 to
	  40.

2004-01-26 04:21  twu

	* src/stage1.c: Sampling exhaustively on short sequences.

2004-01-26 04:20  twu

	* src/: gmap.c, snap.c, stage1.h: Changed criterion for good
	  alignment on short sequences to be based on coverage rather than
	  percent identity.

2004-01-26 04:19  twu

	* src/stage2.c: Removed tiebreaker based on genomic distance.
	  Ignoring gendistance penalty if no better score can be found,
	  which allows program to find distant 5' exons.

2004-01-26 04:15  twu

	* src/: pair.c, pairpool.c, stage3.c: Restored large gap and '#'
	  character when queryjump exceeds maxlookback.

2004-01-26 04:12  twu

	* src/match.c: Fixed bug where accessions were looked up on
	  chromosomal coordinates instead of universal coordinates.

2004-01-26 04:11  twu

	* src/: Makefile.am, datadir.c, datadir.h, snapconfig.c: Removed
	  snapconfig and run-time configuration of SNAP, which doesn't work
	  on statically built binaries.

2004-01-23 09:06  twu

	* src/: gmap.c, snap.c: Updated print_usage statement for non-popt
	  systems.

2004-01-23 08:29  twu

	* src/snapconfig.c: Added a usage statement.

2004-01-23 08:29  twu

	* src/iit_dump.c: Added a debug flag.

2004-01-23 08:29  twu

	* src/iit-write.c: Writing out elements of structs individually,
	  instead of depending on an fwrite of the struct.

2004-01-23 08:28  twu

	* src/: iit-read.c, iit-read.h: Fixed problem with Bigendian reads
	  of iit files.  Added IIT_debug function.

2004-01-23 08:25  twu

	* src/Makefile.am: Provided different dist and nodist instructions
	  depending on FULLDIST.

2004-01-23 01:31  twu

	* src/stage1.c: Set maxentries during sampling to be 10 times that
	  of scanning.	Set stage1size for short sequences to be 12-mers
	  for < 40 nt, and 18-mers for 40-80 nt.

2004-01-23 01:30  twu

	* src/: pair.c, pair.h: Removed '#' is a character in alignment.

2004-01-23 01:28  twu

	* src/: stage3.c, dynprog.c, dynprog.h: Treated cDNA gaps (extra
	  cDNA material) in a way analogous to genome gaps.

2004-01-23 01:24  twu

	* src/pairpool.c: Removed '#' is a character in alignment.

2004-01-23 01:23  twu

	* src/get-genome.c: Changed name of function from isnumber to
	  isnumberp to avoid name conflict with some systems (like MacOSX)
	  that define isnumber in ctype.h.

2004-01-20 10:09  twu

	* src/stage3.c: Fixed bug where dynamic programming of ends
	  wouldn't go all the way to the end of the genomic segment.

2004-01-20 10:09  twu

	* src/dynprog.c: Fixed debug statement.

2004-01-20 08:49  twu

	* src/Makefile.am: Added file matchdef.h

2004-01-20 08:48  twu

	* src/stage1.c: Added a second maxentries parameter to prevent
	  slowness on long repeated inputs, like CA...CA.

2004-01-20 08:47  twu

	* src/: dynprog.c, dynprog.h, pair.c, pair.h, gmap.c, snap.c,
	  stage3.c, stage3.h, params.c, params.h: Added parameter for
	  length of intron gap shown.

2004-01-19 13:15  twu

	* src/stage3.c: Allowed cDNA direction to be indeterminate.

2004-01-19 13:15  twu

	* src/: matchpair.c, stage1.c: Fixed clustering to work with
	  minsize of 1.

2004-01-19 13:14  twu

	* src/dynprog.c: Reduced points for match, which improves some
	  alignments.

2004-01-16 08:29  twu

	* src/: params.c, params.h, gmap.c, snap.c, stage1.c, stage1.h:
	  Removed nsamples as a global parameter.

2004-01-16 08:25  twu

	* bootstrap, configure.ac, src/Makefile.am: Added libtool and
	  --enable-static-linking feature.

2004-01-16 08:24  twu

	* src/: gmap.c, snap.c: Implemented incremental clustering based on
	  progressively smaller sampling intervals.  Added ability to print
	  alignment continuously.

2004-01-16 08:22  twu

	* src/: matchpair.c, matchpair.h, stage1.c: Implemented incremental
	  clustering based on progressively smaller sampling intervals.

2004-01-16 08:21  twu

	* src/: match.c, matchdef.h: Moved structure definition to
	  matchdef.h

2004-01-16 08:20  twu

	* src/: reader.c, reader.h, block.c, block.h: Added ability to
	  reset ends of block.

2004-01-16 01:45  twu

	* src/: stage3.c, stage3.h: Added printing of number of unknowns
	  and of gap openings in cDNA and genome.

2004-01-16 01:44  twu

	* src/: params.c, params.h: Added parameter for continuous output
	  of alignment.

2004-01-16 01:44  twu

	* src/: pair.c, pair.h: Added output of number of unknowns.  Added
	  procedure for continuous output of alignment.

2004-01-16 01:43  twu

	* src/dynprog.c: Created different penalties for gaps in single and
	  paired gaps.

2004-01-14 03:57  twu

	* configure.ac: Added feature for static linking.

2004-01-14 03:54  twu

	* src/: params.c, params.h: Using two parameters for stutter:
	  stuttercycles and stutterhits.

2004-01-14 03:53  twu

	* src/: gmap.c, snap.c: Performing sampling only when necessary.
	  Using popt help when available.

2004-01-14 03:53  twu

	* src/: stage1.c, stage1.h: Performing sampling only when
	  necessary.  Limiting size and changing parameters for bestlist.

2004-01-14 03:42  twu

	* src/: matchpair.c, matchpair.h: Eliminated unused code in
	  filtering procedure.

2004-01-14 03:41  twu

	* src/indexdb.c: Fixed fread_int to be fread_uint.

2004-01-14 03:41  twu

	* src/iit-read.c: Added abort statement when more than one interval
	  retrieved by IIT_get_one.

2004-01-14 03:40  twu

	* src/get-genome.c: Fixed bug with accessing chromosome_iit after
	  being freed.	Using popt help when available.

2004-01-14 03:36  twu

	* src/: oligo.c, oligo.h: Added Oligo_skip function.

2004-01-14 03:35  twu

	* src/: block.c, block.h: Removed maxtries and added Block_skip.

2004-01-12 09:15  twu

	* src/: stage1.c, gmap.c, snap.c: Changed strategy to use clusters
	  of matches, after first pair found.

2004-01-12 09:14  twu

	* src/: gmapindex.c, snapindex.c: Eliminated check for genome
	  database in compression mode.

2004-01-12 09:13  twu

	* src/stage2.c: Changed distance penalty to 1 point per 1000 nt.

2004-01-12 09:13  twu

	* src/: pair.c, pair.h, stage3.c: Keeping separate track of query
	  indels and target indels.

2004-01-12 09:12  twu

	* src/: genome.c, genome.h, get-genome.c: Implemented check for
	  gbufferlen when shifting old sequence.

2004-01-12 08:54  twu

	* src/separator.h: Added file for separator information.

2004-01-09 07:13  twu

	* src/genome.c: Fixed bug from call to madvise on NULL region.

2004-01-09 07:13  twu

	* src/: get-genome.c, Makefile.am: Changed program to use
	  chromosome_iit and contig_iit, rather than text files.

2004-01-09 07:12  twu

	* src/: iit-read.c, iit-read.h: Added function IIT_read_linear.

2004-01-09 07:12  twu

	* src/: gmapindex.c, snapindex.c: Storing length in interval of
	  contig_iit, rather than in annotation.

2004-01-09 07:11  twu

	* src/stage1.c: Changed paired algorithm to use sum of reciprocals
	  of number of hits.

2004-01-09 04:07  twu

	* src/get-genome.c: Removed unnecessary decompression functions
	  (now in genome.c).

2004-01-09 04:03  twu

	* src/: gmap.c, snap.c: Fixed bug where fraction_threshold was
	  declared as int rather than double.

2004-01-09 04:03  twu

	* src/stage1.c: Revised algorithm to count number of query hits on
	  5' and 3' ends.

2004-01-09 02:16  twu

	* src/get-genome.c: Moved datadir functions to a separate file.

2004-01-09 02:12  twu

	* src/: gmapindex.c, snapindex.c: Changed format of text files
	  .chromosome and .contig.

2004-01-09 02:11  twu

	* src/: datadir.c, datadir.h, gmap.c, snap.c, snapconfig.c,
	  Makefile.am: Moved datadir functions to a separate file.

2004-01-08 05:45  twu

	* src/: gmap.c, snap.c: Allowed genomic patches to be longer or
	  shorter than their endpoints.

2004-01-08 05:44  twu

	* src/: gmapindex.c, snapindex.c: Allowed intervals to have length
	  that is different from their endpoints.  Changed format for fasta
	  file input to snapindex.

2004-01-08 05:43  twu

	* src/iit-read.c: Added carriage returns to annotations, if absent.

2004-01-08 05:42  twu

	* src/: get-genome.c, iit-write.c, iit-write.h, genome.c, genome.h:
	  Allowed genomic patches to be longer or shorter than their
	  endpoints.

2004-01-08 05:41  twu

	* src/: interval.c, interval.h, segmentpos.c, segmentpos.h,
	  iit_store.c: Allowed intervals to have length that is different
	  from their endpoints.

2004-01-07 06:00  twu

	* src/: gmap.c, snap.c, params.c, params.h: Made fraction_threshold
	  a parameter.

2004-01-07 02:14  twu

	* src/stage2.c: Changed calculation of penalty for large genome
	  distances to be done only when necessary.

2004-01-07 02:13  twu

	* src/snapconfig.c: Changed feedback message.

2004-01-07 02:12  twu

	* src/: genome.c, indexdb.c: Improved warning messages when memory
	  mapping fails.

2004-01-05 07:35  twu

	* src/snapdir.c: Changed name of snapdir to snapconfig.

2004-01-05 05:51  twu

	* src/: stage1.c, stage1.h: Moved decision of stage1size and
	  maxentries to here.

2004-01-05 05:51  twu

	* src/: match.c, match.h, gmap.c, snap.c, result.c, result.h,
	  params.c, params.h: Restored alignment using stage 1 only.

2004-01-05 05:50  twu

	* src/genome.c: Added warning message of memory mapping of genome
	  fails.

2004-01-05 05:45  twu

	* src/genome.c: Restored batch memory mapping of genome.

2004-01-05 02:03  twu

	* src/stage1.c: Greatly increased MAXENTRIES parameter.

2004-01-05 02:02  twu

	* src/: params.c, params.h, gmap.c, snap.c: Made stage1size
	  dependent upon sequence length, with short sequences getting
	  stage1size of 12.

2004-01-05 01:21  twu

	* util/: gmap_compress.pl, gmap_compress.pl.in, snap_compress.pl,
	  whats_on: Generalized parse for coordinate separator.

2004-01-05 01:19  twu

	* src/get-genome.c: Restored -- as coordinate separator.

2003-12-19 14:58  twu

	* src/: gmap.c, snap.c, sequence.c, sequence.h, stage3.c, stage3.h:
	  New approach to chimeras, involving a subsequence and new stage1
	  procedure.

2003-12-19 14:56  twu

	* src/stage2.c: Added distance penalty for long introns.

2003-12-19 14:55  twu

	* src/: Makefile.am, pair.c, segmentpos.c: Included separator.h

2003-12-19 04:08  twu

	* src/: pair.c, segmentpos.c, segmentpos.h: Removed unnecessary
	  parameters in Segmentpos_print_accessions.

2003-12-19 04:08  twu

	* src/get-genome.c: Change in coordinate separator from -- to ..

2003-12-17 07:04  twu

	* src/: pair.c, segmentpos.c: Changing coordinate output from -- to
	  ..

2003-12-17 07:04  twu

	* src/: stage3.c, stage3.h: Changed procedures for finding chimeras
	  to try singlelist of the appropriate side.  Fixed bug in
	  computing chimeric goodness.

2003-12-17 07:03  twu

	* src/: gmap.c, snap.c, stage1.c, stage1.h, match.c, match.h,
	  matchpair.c, matchpair.h: Changed procedures for finding chimeras
	  to try singlelist of the appropriate side.

2003-12-17 07:02  twu

	* src/: dynprog.c, dynprog.h: Provided separate parameters for
	  ends, removed multiplicative reward, and changed all score
	  calculations to be integers.

2003-12-16 04:31  twu

	* src/: matchpair.c, stage1.c, stage1.h: Fixed bug with position
	  calculations on large chromosomes (> 2 Gig).

2003-12-16 02:10  twu

	* src/: stage1.c, stage1.h, gmap.c, snap.c, matchpair.c,
	  matchpair.h: Based algorithm for finding extensions on 12-mers.

2003-12-16 02:09  twu

	* src/: chrnum.c, chrnum.h: Added function for computing
	  chromosomal string and position from genomic position.

2003-12-15 06:15  twu

	* src/: stage1.c, stage1.h: Made cluster list depend on size of
	  largest cluster.

2003-12-15 06:14  twu

	* src/: matchpair.c, matchpair.h, gmap.c, snap.c, params.c,
	  params.h: Made extension linear depending on query length.

2003-12-14 00:05  twu

	* src/stage2.c: Added a minimum exon length for ends during
	  smoothing.

2003-12-13 23:24  twu

	* src/: stage1.c, stage1.h: Added a last-resort procedure for
	  trying all matches found in stage 1.	Enhanced debugging
	  statements.

2003-12-13 23:24  twu

	* src/: gmap.c, snap.c: Added a last-resort procedure for trying
	  all matches found in stage 1.

2003-12-13 23:22  twu

	* src/: genome.c, genome.h, get-genome.c: Enhanced debugging
	  statements.

2003-12-13 23:21  twu

	* src/matchpair.c: Added assertions about strands and relative
	  position of matches.

2003-12-13 23:20  twu

	* src/: oligoindex.c, shortoligomer.h: Returned to old method for
	  store_positions, because it appears to be faster.

2003-12-13 23:18  twu

	* src/stage2.c: Returned to old method for store_positions.  Fixed
	  smoothing for a single exon.

2003-12-13 01:27  twu

	* src/: oligoindex.c, shortoligomer.h, types.h: Further attempt to
	  increase speed of store_positions.

2003-12-13 00:45  twu

	* src/: gmap.c, snap.c: Fixed memory leak when stage3array is
	  recomputed.

2003-12-13 00:44  twu

	* src/: oligoindex.c, oligoindex.h, stage2.c: Increasing speed of
	  store_positions by reducing number of calls to calloc.

2003-12-12 22:13  twu

	* src/: stage1.c, stage1.h, matchpair.c, matchpair.h, params.c,
	  params.h, gmap.c, snap.c: Changed cluster algorithm to rank
	  clusters based on size and process the top ones based on sum of
	  sizes.

2003-12-12 14:50  twu

	* src/genome.c: Added check for enddiscard being 0.

2003-12-12 14:43  twu

	* src/stage2.c: Did an in-lining of intron_score.

2003-12-12 10:34  twu

	* src/: gmap.c, params.c, params.h, snap.c, stage1.c, stage1.h,
	  stage3.c, stage3.h: Added new cluster algorithm for stage 1, used
	  when paired algorithm fails to produce an alignment with high
	  identity.

2003-12-12 05:29  twu

	* src/: gmap.c, snap.c: Added ability to modify binary file to
	  include default genome directory.

2003-12-12 05:27  twu

	* src/: snapconfig.c, snapdir.c: Initial import into CVS.

2003-12-10 04:30  twu

	* src/: gmapindex.c, snapindex.c, indexdb.c, indexdb.h: Added
	  ability to generate idxoffsets and idxpositions files from
	  compressed genome.

2003-12-10 04:30  twu

	* src/: gmap.c, snap.c: Changed the uncompressed flag from -G to
	  -g.

2003-12-09 17:42  twu

	* src/: gmapindex.c, snapindex.c: Implemented direct writing of
	  compressed genome file.

2003-12-09 09:43  twu

	* src/iit_store.c: Fixed bug where non-copied string is entered
	  into table.

2003-12-09 09:42  twu

	* src/iit_get.c: Improved error message.

2003-12-09 09:42  twu

	* src/iit_dump.c: Added function for showing all types.

2003-12-09 09:42  twu

	* src/table.c: Added debugging statements.

2003-12-09 09:41  twu

	* src/: sequence.c, sequence.h: Restored function Sequence_revcomp.

2003-12-09 09:41  twu

	* src/: gmap.c, snap.c, params.c, params.h: For user-provided
	  segments, skipping stage 1 (although can be specified by the
	  user), to achieve increased speed.

2003-12-04 02:27  twu

	* src/stage1.c: Restored cluster algorithm for short sequences.

2003-12-04 02:27  twu

	* src/: gmap.c, snap.c: Generalized definition of chimera, and
	  reduced percentage to 80%.

2003-12-03 05:42  twu

	* src/: iit_get.c, iit-read.c, iit-read.h, Makefile.am: Augmented
	  iit_get to handle types and file input.

2003-12-03 05:41  twu

	* src/: sequence.c, sequence.h, gmap.c, snap.c, intlist.c,
	  intlist.h: Allowed user-specified genomic segment to have
	  arbitrary length.

2003-12-02 21:42  twu

	* src/: gmap.c, snap.c: Restored -U flag for reporting in universal
	  coordinates.

2003-12-02 21:42  twu

	* src/iit-read.c: Fixed bug in IIT_dump_formatted.

2003-12-02 21:41  twu

	* src/: md5-compute.c, Makefile.am: Added program md5-compute.

2003-12-01 08:37  twu

	* src/: gmap.c, snap.c, params.c, params.h: Added message to user
	  when FASTA file is run without batch mode.

2003-11-28 11:50  twu

	* src/oligo.c: Changed debug statements.

2003-11-28 11:50  twu

	* src/reader.c: Cleaned up pointer calculation.

2003-11-28 11:49  twu

	* src/sequence.h: Removed Sequence_revcomp, which is not used.

2003-11-28 11:49  twu

	* src/sequence.c: Revised comments.

2003-11-28 11:49  twu

	* src/stage2.c: In-lined gap_score.

2003-11-28 03:50  twu

	* src/indexdb.c: More bug fixes for bigendian machines on
	  user-provided segments.

2003-11-28 03:37  twu

	* src/indexdb.c: Fixed a problem with bigendian machines for
	  user-provided segments.

2003-11-28 01:19  twu

	* src/: gmap.c, snap.c: Added releasestring in attempt to find
	  version file.

2003-11-28 01:19  twu

	* src/: genome.c, genome.h: Added option for replacing X's with
	  N's.

2003-11-28 01:19  twu

	* src/get-genome.c: Added option for replacing X's with N's.  Fixed
	  bug when closing a null file pointer.

2003-11-28 01:18  twu

	* src/iit_store.c: Append .iit to given filename, instead of
	  replacing existing suffix.

2003-11-26 07:12  twu

	* src/: gmapindex.c, snapindex.c: Removed -U flag.

2003-11-26 07:11  twu

	* src/: indexdb.c, indexdb.h, gmapindex.c, snapindex.c: Reverted
	  back to using uncompressed genome for making idxoffsets and
	  idxpositions.

2003-11-26 07:11  twu

	* src/: gmap.c, snap.c: Changed flag for uncompressed genome from
	  -G to -U.

2003-11-26 07:01  twu

	* src/: gmapindex.c, indexdb.c, indexdb.h, snapindex.c: Attempt to
	  build idxoffsets and idxpositions from genomecomp, but has
	  problems.

2003-11-25 22:15  twu

	* src/genome.c: Added automated switching between compressed and
	  uncompressed genome, if the requested one cannot be found.

2003-11-25 22:01  twu

	* src/iit_store.c: Keeping last carriage return of annotation.

2003-11-25 22:01  twu

	* src/iit_get.c: If iit file cannot be found, try appending .iit.

2003-11-25 22:00  twu

	* src/: gmapindex.c, snapindex.c: Finding labels in IIT directly
	  instead of converting to a table.

2003-11-25 21:54  twu

	* src/: iit-read.c, iit-read.h, iit-write.c, iitdef.h: Changed IIT
	  format to store alphabetic order of labels, so that labels can be
	  found by binary search.

2003-11-25 12:58  twu

	* src/: genome.c, genome.h, pair.c, pair.h, params.c, params.h,
	  gmap.c, snap.c, stage3.c, stage3.h: Added popt handling of
	  options.  Renamed various program options.

2003-11-25 12:57  twu

	* src/: iit-read.c, iit-read.h, iit_get.c: Added ability to search
	  IITs by label.

2003-11-25 12:56  twu

	* src/get-genome.c: Changed usage statement for popt autohelp.

2003-11-25 12:55  twu

	* src/Makefile.am: Changed name of variable to POPT_LIBS.

2003-11-25 12:55  twu

	* acinclude.m4, configure.ac: Added AC_DEFINE for HAVE_LIBPOPT.
	  Set various defines to have value 1.

2003-11-25 04:57  twu

	* src/: iit-read.c, iit-read.h, iit-write.c, iit-write.h,
	  iit_get.c, iit_store.c, iitdef.h, gmapindex.c, match.c,
	  segmentpos.c, snapindex.c: Change made to format of IIT file.
	  Now allowing each interval to be labeled.

2003-11-25 04:56  twu

	* src/indexdb.c: Fix made for the case where an oligomer earlier
	  than TT...TT is the last one and points to totalcounts.

2003-11-24 10:12  twu

	* util/: gmap_compress.pl, gmap_compress.pl.in, snap_compress.pl:
	  Added notation for chimeric sequences.

2003-11-24 10:12  twu

	* acinclude.m4: Added check for MAP_FAILED.  Added sys/types.h when
	  checking for pthreads (needed for Sun compiler).

2003-11-24 10:02  twu

	* src/: assert.h, bigendian.h, blackboard.h, block.h, chrnum.h,
	  complement.h, dynprog.h, except.h, genome.h, genomicpos.h,
	  iit-read.h, iit-write.h, indexdb.h, interval.h, intlist.h,
	  intron.h, list.h, match.h, matchpair.h, md5.h, mem.h, oligo.h,
	  oligoindex.h, pair.h, pairpool.h, params.h, reader.h, reqpost.h,
	  request.h, result.h, segmentpos.h, sequence.h, stage1.h,
	  stage2.h, stage3.h, stopwatch.h, table.h, uintlist.h,
	  iit-write.c, iit_dump.c, iit_get.c, iit_store.c: Included
	  config.h in all header files, to catch redefinition of const,
	  which is needed for the Sun compiler.

2003-11-24 10:00  twu

	* src/stage3.c: Commented out code that is never reached.

2003-11-24 09:59  twu

	* src/: genome.c, indexdb.c: Modified messages to stderr for batch
	  mode.

2003-11-24 09:57  twu

	* src/: blackboard.c, reqpost.c, gmap.c, snap.c: Added sys/types.h
	  to handle pthread_t, needed by Sun compiler.

2003-11-24 09:57  twu

	* src/assert.c: Kept only the header file definition of assert, due
	  to problem with Sun compiler.

2003-11-24 09:55  twu

	* src/: table.c, iit-read.c: For functions passed as arguments,
	  added pointer and parentheses around parameter list.

2003-11-24 08:05  twu

	* src/stage2.c: Changed some exon length parameters.

2003-11-19 09:57  twu

	* src/: gmap.c, snap.c, stage3.c, stage3.h: Added additional check
	  for chimeras, based on top two hits.

2003-11-19 08:56  twu

	* src/: bigendian.c, indexdb.c: Moved masking to the logical or
	  statements to address a bug on MacOSX.

2003-11-18 06:34  twu

	* src/: gmap.c, snap.c: Made directory searching process more
	  flexible, by looking for version file at toplevel and
	  subdirectory of datadir.

2003-11-18 06:09  twu

	* src/: genome.c, indexdb.c: Fixed calls to mmap and munmap when
	  mmap fails.  Moved stopwatch start before madvise command.

2003-11-18 04:08  twu

	* src/: bigendian.c, genome.c, indexdb.c: Added masks to chars when
	  converting to an int or unsigned int, due to problem observed on
	  DEC Alpha.

2003-11-18 03:40  twu

	* src/: indexdb.c, genome.c: Corrected conversion of littleendian
	  to bigendian numbers.  Added lseek and read procedures when mmap
	  is not present or fails.

2003-11-18 03:39  twu

	* src/bigendian.c: Corrected conversion of littleendian to
	  bigendian numbers.

2003-11-18 03:39  twu

	* Makefile.am: Generate ChangeLog only when CVS directory present.

2003-11-17 10:32  twu

	* src/Makefile.am: Used LDADD instructions to call libraries
	  instead of LDFLAGS.  (Required for program to load on SGI.)
	  Moved SCRIPTS under FULLDIST.

2003-11-17 10:31  twu

	* configure.ac: Renamed POPT_LDFLAGS to POPT_LIBS.

2003-11-17 10:30  twu

	* bootstrap: Added --copy flag to automake.

2003-11-17 10:30  twu

	* Makefile.am: Added dist-hook to make ChangeLog up to date.

2003-11-17 09:47  twu

	* config/: install-sh, missing, mkinstalldirs: Removed secondary
	  config files generated by automake.

2003-11-17 09:44  twu

	* src/: gmapindex.c, snapindex.c: Fixed bug where X's were not
	  being filled in, because variable declared as int, rather than
	  unsigned int.

2003-11-17 09:43  twu

	* src/: block.c, block.h: Removed obsolete function.

2003-11-17 09:35  twu

	* config/acinclude.m4: Moved to top-level directory.

2003-11-17 07:06  twu

	* ChangeLog: Removed from repository.  Can be generated as needed.

2003-11-17 06:53  twu

	* bootstrap: Added --add-missing flag.

2003-11-17 06:51  twu

	* README: Added message about config.site.

2003-11-17 06:49  twu

	* bootstrap: Initial import into CVS.  Added because autoreconf
	  doesn't work with a config subdirectory.

2003-11-17 06:49  twu

	* configure.ac: Made toplevel configure.ac work with a config
	  subdirectory.

2003-11-17 06:48  twu

	* src/: gmap.c, snap.c, stage1.c, stage1.h: Changed algorithm to
	  declare chimera only after alignment is done, and to use salvaged
	  matches in that case.

2003-11-17 06:47  twu

	* src/: stage3.c, stage3.h: Stored genomicstart and genomicend as
	  part of Stage3_T structure.

2003-11-17 04:26  twu

	* util/ddsgap2_compress.pl: Initial import into CVS.

2003-11-17 04:25  twu

	* whats_on: Moved to subdirectory.

2003-11-17 04:23  twu

	* config.guess, config.sub, compile, depcomp: Removed secondary
	  config files (generated by automake).

2003-11-17 04:21  twu

	* Makefile.am: Adding top-level Makefile.am

2003-11-17 04:15  twu

	* install-sh, missing, mkinstalldirs: Moved to subdirectory.

2003-11-17 04:10  twu

	* sim4_compress.pl, sim4_uncompress.pl, snap_compress.pl,
	  snap_uncompress.pl, spidey_compress.pl, snapbuild.pl.in: Moved to
	  subdirectory.

2003-11-17 03:10  twu

	* assert.c, assert.h, bigendian.c, bigendian.h, blackboard.c,
	  blackboard.h, block.c, block.h, bool.h, chrnum.c, chrnum.h,
	  complement.c, complement.h, dynprog.c, dynprog.h, except.c,
	  except.h, genome.c, genome.h, genomicpos.c, genomicpos.h,
	  genuncompress.c, get-genome.c, iit-read.c, iit-read.h,
	  iit-write.c, iit-write.h, iit_dump.c, iit_get.c, iit_store.c,
	  iitdef.h, indexdb.c, indexdb.h, interval.c, interval.h,
	  intlist.c, intlist.h, intron.c, intron.h, list.c, list.h,
	  listdef.h, match.c, match.h, matchpair.c, matchpair.h, md5.c,
	  md5.h, md5.t.c, mem.c, mem.h, oligo-count.c, oligo.c, oligo.h,
	  oligoindex.c, oligoindex.h, pair.c, pair.h, pairdef.h,
	  pairpool.c, pairpool.h, params.c, params.h, reader.c, reader.h,
	  reqpost.c, reqpost.h, request.c, request.h, result.c, result.h,
	  segmentpos.c, segmentpos.h, sequence.c, sequence.h,
	  shortoligomer.h, snap.c, snapindex.c, stage1.c, stage1.h,
	  stage2.c, stage2.h, stage3.c, stage3.h, stopwatch.c, stopwatch.h,
	  table.c, table.h, types.h, uintlist.c, uintlist.h: Moved source
	  files to subdirectory.

2003-11-17 02:40  twu

	* iit-read.c, src/iit-read.c, iit-read.h, src/iit-read.h: Added
	  function IIT_get_typed.

2003-11-17 02:40  twu

	* indexdb.c, src/indexdb.c: Removed debugging message.

2003-11-17 02:39  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h, snap.c,
	  src/gmap.c, src/snap.c: Improved determination of when an
	  alternate strain applies, based on the aligned genomic segment.
	  Added strain type to sorting of results.

2003-11-17 02:38  twu

	* stage1.c, src/stage1.c: Bypassing the cluster algorithm.

2003-11-16 22:43  twu

	* snap.c, src/gmap.c, src/snap.c: Added ability to determine
	  datadir from environment variable or configuration file.

2003-11-16 22:43  twu

	* get-genome.c, src/get-genome.c: Added popt processing of
	  command-line options.

2003-11-16 22:42  twu

	* genome.c, src/genome.c: Added bigendian conversions for
	  compressed genome, which is memory mapped.

2003-11-16 22:41  twu

	* configure.ac, src/Makefile.am: Added check for popt library.

2003-11-14 22:35  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Fixed pointer bug.

2003-11-14 22:34  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h: Removed
	  directional check on stage 2 smoothing.  Introduced separate
	  length criterion for first long exon.

2003-11-14 22:33  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h: Implemented
	  checks and procedures for chimeric sequences.  Removed
	  directional check on stage 2 smoothing.

2003-11-14 22:30  twu

	* pair.c, src/pair.c, pair.h, src/pair.h, result.c, src/result.c,
	  result.h, src/result.h, stage1.c, src/stage1.c, stage1.h,
	  src/stage1.h, snap.c, src/gmap.c, src/snap.c: Implemented checks
	  and procedures for chimeric sequences.

2003-11-14 22:28  twu

	* genome.c, src/genome.c: Changed debug statements from stderr to
	  stdout.

2003-11-14 12:31  twu

	* stage1.c, src/stage1.c: Changed identify_matches to assume the
	  absence of duplicates.

2003-11-14 12:08  twu

	* stage2.c, src/stage2.c: Changed criterion for short first and
	  last exon during smoothing to be half of the corresponding
	  region.

2003-11-14 12:04  twu

	* stage3.c, src/stage3.c: Fixed debugging statements.

2003-11-14 06:19  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h, snap.c,
	  src/gmap.c, src/snap.c: Fixed bug where a strain was falsely
	  reported due to duplicate stage 3 objects and deletion of the one
	  for the reference.

2003-11-14 06:18  twu

	* sequence.c, src/sequence.c: Reduced poly-A tail left from 7 to 1.

2003-11-14 06:17  twu

	* pair.c, src/pair.c: Made print procedure backward compatible with
	  old altstrain_iits.

2003-11-14 05:05  twu

	* pair.c, params.c, params.h, snap.c, snapindex.c, src/gmap.c,
	  src/gmapindex.c, src/pair.c, src/params.c, src/params.h,
	  src/snap.c, src/snapindex.c: Made changes to include name of
	  reference strain.

2003-11-13 23:21  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed typo in comment.

2003-11-13 23:21  twu

	* iit-read.c, src/iit-read.c: Fixed memory leak when altstrain_iit
	  doesn't exist.

2003-11-13 23:21  twu

	* src/Makefile.am: Integrated get-genome into snap code.

2003-11-13 23:20  twu

	* get-genome.c, src/get-genome.c, sequence.c, src/sequence.c,
	  sequence.h, src/sequence.h: Major rewrite of get-genome, to
	  integrate it into existing snap code.

2003-11-13 21:52  twu

	* snap.c, src/gmap.c, src/snap.c, genome.c, src/genome.c, genome.h,
	  src/genome.h: Handled case where more than one patch from a given
	  strain is applicable to a given genomic segment.

2003-11-13 21:51  twu

	* intlist.c, src/intlist.c: Added check for null list in
	  Intlist_to_array.

2003-11-13 21:51  twu

	* indexdb.c, src/indexdb.c: Changed idxpositions to eliminate
	  duplicates during writing and to skip bad values during reading.

2003-11-13 10:12  twu

	* snap_compress.pl, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/snap_compress.pl: Revised program
	  to parse strain info.

2003-11-13 10:12  twu

	* stage1.c, src/stage1.c: Added some comments.

2003-11-13 10:11  twu

	* oligo-count.c, src/oligo-count.c, oligo.c, src/oligo.c, oligo.h,
	  src/oligo.h, block.c, src/block.c, block.h, src/block.h,
	  src/Makefile.am: Revised oligo-count to use the new code.

2003-11-13 03:58  twu

	* src/Makefile.am: Added build for get-genome.

2003-11-13 03:57  twu

	* get-genome.c, src/get-genome.c: Major cleaning of code.  Added
	  ability to read from compressed genome files.

2003-11-13 03:56  twu

	* oligo-count.c, src/oligo-count.c: Initial import into CVS.  Dated
	  2003-07-16.

2003-11-12 23:37  twu

	* genome.c, genome.h, genomicpos.c, genomicpos.h, matchpair.c,
	  matchpair.h, pair.c, pair.h, snap.c, src/genome.c, src/genome.h,
	  src/genomicpos.c, src/genomicpos.h, src/gmap.c, src/matchpair.c,
	  src/matchpair.h, src/pair.c, src/pair.h, src/snap.c, stage3.c,
	  stage3.h, src/stage3.c, src/stage3.h: Added ability to align to
	  multiple strains.

2003-11-12 23:36  twu

	* stage1.c, src/stage1.c: Cleaned up some bugs on handling stutter.
	  Implemented check for duplicates in idxpositions.

2003-11-12 23:33  twu

	* indexdb.c, src/indexdb.c, indexdb.h, src/indexdb.h, snapindex.c,
	  src/gmapindex.c, src/snapindex.c: Changed strategy for idxoffsets
	  and idxpositions for strains.  Now storing the union of all
	  strains.

2003-11-12 15:58  twu

	* snapbuild.pl.in, src/gmapsetup.pl.in, src/snapbuild.pl.in,
	  util/gmap_setup.pl.in, src/Makefile.am: Fixed procedure for
	  making snapbuild.

2003-11-12 15:51  twu

	* src/Makefile.am: Added procedure for making snapbuild script.

2003-11-12 15:50  twu

	* configure.ac: Added feature for enabling full distribution.

2003-11-12 05:20  twu

	* snapbuild.pl: Changed file from snapbuild.pl to snapbuild.pl.in.

2003-11-12 05:17  twu

	* src/Makefile.am, configure.ac, params.h, src/params.h: Cleaned up
	  specification of data directory and version file.

2003-11-12 05:17  twu

	* params.c, src/params.c: Added provisions for reading altstrain
	  IIT.

2003-11-12 05:16  twu

	* snap.c, src/gmap.c, src/snap.c: Cleaned up specification of data
	  directory and version file.  Added provisions for reading
	  altstrain IIT.

2003-11-12 04:59  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Fixed problem with
	  slashes in alternate strain name.

2003-11-12 04:58  twu

	* stage1.c, src/stage1.c: Cleaned up code for stage1.c.  Fixed
	  memory leak for paired algorithm.  Added chromosomal constraint
	  for cluster algorithm.

2003-11-11 09:13  twu

	* iit-read.c, iit-read.h, iit-write.c, src/Makefile.am,
	  src/iit-read.c, src/iit-read.h, src/iit-write.c, iit-write.h,
	  iit_dump.c, iit_get.c, iit_store.c, iitdef.h, indexdb.c,
	  indexdb.h, interval.c, interval.h, src/iit-write.h,
	  src/iit_dump.c, src/iit_get.c, src/iit_store.c, src/iitdef.h,
	  src/indexdb.c, src/indexdb.h, src/interval.c, src/interval.h,
	  segmentpos.c, segmentpos.h, snap.c, snapbuild.pl,
	  snapbuild.pl.in, snapindex.c, src/gmap.c, src/gmapindex.c,
	  src/gmapsetup.pl.in, src/segmentpos.c, src/segmentpos.h,
	  src/snap.c, src/snapbuild.pl.in, src/snapindex.c,
	  util/gmap_setup.pl.in: Changes made to introduce types into IITs,
	  and to build SNAP databases with alternate strain information.

2003-11-11 08:50  twu

	* stage1.c, src/stage1.c, match.c, match.h, src/match.c,
	  src/match.h: Changes to stage 1 algorithm: (1) choice of 5' or 3'
	  advancement based on number of hits, (2) stutter based on
	  positions with hits, (3) computed fraction of paired hits on each
	  end.

2003-11-10 09:58  twu

	* snapbuild.pl, snapbuild.pl.in, src/gmapsetup.pl.in,
	  src/snapbuild.pl.in, util/gmap_setup.pl.in: Initial import into
	  CVS.

2003-11-10 09:51  twu

	* src/Makefile.am: Added object files for bigendian.

2003-11-10 09:51  twu

	* iit-read.c, src/iit-read.c: Added header file for bigendian.h

2003-11-10 09:50  twu

	* indexdb.c, src/indexdb.c, bigendian.c, src/bigendian.c: Fixed
	  problem in bigendian conversion.

2003-11-10 09:50  twu

	* sequence.c, src/sequence.c: Fixed problem in handling sequence
	  files without headers.

2003-11-10 04:28  twu

	* iit-read.c, src/iit-read.c: Changed most elements of IIT_T to be
	  fread, rather than mmapped.  Added code for program to work on
	  bigendian architectures.

2003-11-10 04:27  twu

	* indexdb.c, src/indexdb.c: Changed offsets file to be fread,
	  rather than mmapped.	Added code for program to work on bigendian
	  architectures.

2003-11-10 04:27  twu

	* iitdef.h, src/iitdef.h: Added comments.

2003-11-10 04:24  twu

	* bigendian.c, bigendian.h, src/Makefile.am, src/bigendian.c,
	  src/bigendian.h, configure.ac, genuncompress.c,
	  src/genuncompress.c, iit-write.c, src/iit-write.c, snapindex.c,
	  src/gmapindex.c, src/snapindex.c: Added code for program to work
	  on bigendian architectures.

2003-11-08 02:41  twu

	* acinclude.m4, config/acinclude.m4, configure.ac: Made VERSION
	  automatically equal the current date.

2003-11-08 02:28  twu

	* src/Makefile.am: Removed reference to iit_convert.

2003-11-08 02:28  twu

	* genome.c, src/genome.c: Turned off batch loading of genome.

2003-11-08 00:05  twu

	* sequence.c, src/sequence.c, snap.c, src/gmap.c, src/snap.c: Rest
	  of header printed in output.	Exceptional file terminations
	  handled better.

2003-11-07 15:12  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h, params.c,
	  src/params.c, params.h, src/params.h, snap.c, src/gmap.c,
	  src/snap.c: Added cluster algorithm for short query sequences.

2003-11-07 15:09  twu

	* oligo.c, src/oligo.c, oligo.h, src/oligo.h, longoligomer.h,
	  longoligomer.c, block.c, src/block.c, block.h, src/block.h,
	  src/Makefile.am, match.c, src/match.c, match.h, src/match.h,
	  matchpair.c, src/matchpair.c, matchpair.h, src/matchpair.h:
	  Removed longoligomers.

2003-11-07 11:19  twu

	* genome.c, src/genome.c: Fixed print statement for batch mode.

2003-11-07 04:55  twu

	* snap.c, src/gmap.c, src/snap.c: Restored dump_segs functionality.

2003-11-07 04:54  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Changed name of
	  table from chroffset to chrlength.

2003-11-07 04:54  twu

	* iit-read.c, src/iit-read.c, iit-read.h, src/iit-read.h: Added
	  function IIT_dump_formatted.

2003-10-27 04:58  twu

	* iit_get.c, src/iit_get.c, iit_store.c, src/iit_store.c: Removed
	  carriage return at end of annotation.

2003-10-27 04:57  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Added better
	  comments.

2003-10-27 04:57  twu

	* whats_on, util/whats_on: Fixed program to use new IIT file
	  format.

2003-10-27 04:56  twu

	* table.c, src/table.c: Removed assertion checks for key being
	  non-zero, which doesn't work for a chromosome of 0.

2003-10-27 04:56  twu

	* INSTALL: Copied generic installation instructions.

2003-10-27 04:56  twu

	* COPYING: Created copyright notice.

2003-10-27 04:55  twu

	* iit_dump.c, src/Makefile.am, src/iit_dump.c, iit-read.c,
	  src/iit-read.c, iit-read.h, src/iit-read.h: Added a program for
	  dumping IIT files.

2003-10-24 23:42  twu

	* iit-write.c, src/iit-write.c: Made Node_make static.

2003-10-24 05:20  twu

	* indexdb.c, src/indexdb.c: Fixed format of batch statement.

2003-10-24 05:16  twu

	* iit-read.c, src/iit-read.c, iit-write.c, src/iit-write.c,
	  iit_get.c, src/iit_get.c, match.c, src/match.c, segmentpos.c,
	  src/segmentpos.c, snapindex.c, src/gmapindex.c, src/snapindex.c:
	  Changed annotations in .iit files to have '\0' characters at the
	  ends, so they can be used in the file, without copying.

2003-10-23 10:56  twu

	* interval.c, src/interval.c: Added comment about sorting
	  procedures.

2003-10-23 10:56  twu

	* iit_store.c, src/iit_store.c, iit_get.c, src/iit_get.c: Changed
	  program to use the IIT implementation in this directory.

2003-10-23 10:55  twu

	* iit-read.c, src/iit-read.c: Added madvise command.

2003-10-23 10:54  twu

	* genome.c, src/genome.c, indexdb.c, src/indexdb.c: Changed
	  reporting of touching pages under batch mode.

2003-10-23 10:54  twu

	* src/Makefile.am: Added iit_store and iit_get.

2003-10-23 08:30  twu

	* genome.c, src/genome.c, indexdb.c, src/indexdb.c: Revised
	  touching of pages for batch mode.

2003-10-23 00:57  twu

	* assert.h, blackboard.h, block.h, bool.h, chrnum.h, complement.h,
	  dynprog.h, except.h, genome.h, genomicpos.h, iit-read.h,
	  iit-write.h, iitdef.h, indexdb.h, interval.h, intlist.h,
	  intron.h, list.h, listdef.h, longoligomer.h, match.h,
	  matchpair.h, md5.h, mem.h, oligo.h, src/assert.h,
	  src/blackboard.h, src/block.h, src/bool.h, src/chrnum.h,
	  src/complement.h, src/dynprog.h, src/except.h, src/genome.h,
	  src/genomicpos.h, src/iit-read.h, src/iit-write.h, src/iitdef.h,
	  src/indexdb.h, src/interval.h, src/intlist.h, src/intron.h,
	  src/list.h, src/listdef.h, src/match.h, src/matchpair.h,
	  src/md5.h, src/mem.h, src/oligo.h, oligoindex.h, pair.h,
	  pairdef.h, pairpool.h, params.h, reader.h, reqpost.h, request.h,
	  result.h, segmentpos.h, sequence.h, shortoligomer.h, stage1.h,
	  stage2.h, stage3.h, stopwatch.h, table.h, types.h, uintlist.h,
	  src/oligoindex.h, src/pair.h, src/pairdef.h, src/pairpool.h,
	  src/params.h, src/reader.h, src/reqpost.h, src/request.h,
	  src/result.h, src/segmentpos.h, src/sequence.h,
	  src/shortoligomer.h, src/stage1.h, src/stage2.h, src/stage3.h,
	  src/stopwatch.h, src/table.h, src/types.h, src/uintlist.h: Added
	  RCS Id string to header files.

2003-10-23 00:53  twu

	* snap.c, src/gmap.c, src/snap.c: Removed call to strdup.

2003-10-23 00:53  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Removed printing
	  of superaccessions for NCBI genomes.

2003-10-23 00:52  twu

	* segmentpos.c, src/segmentpos.c: Removed unused procedures based
	  on Berkeley DB.

2003-10-23 00:52  twu

	* chrnum.c, src/chrnum.c: Fixed problem with numeric-alpha ordering
	  of chromosomes.  XU now follows X and precedes Y.

2003-10-22 15:12  twu

	* config.h.in: Removed derived file.

2003-10-22 15:11  twu

	* acinclude.m4, config/acinclude.m4, genome.c, src/genome.c,
	  indexdb.c, src/indexdb.c: Added macros to check for pagesize
	  determination.

2003-10-22 15:11  twu

	* configure.ac: Cleaned up unnecessary autoconf macros.

2003-10-22 13:35  twu

	* acinclude.m4, config.h.in, genome.c, genuncompress.c, iit-read.c,
	  indexdb.c, config/acinclude.m4, src/genome.c,
	  src/genuncompress.c, src/iit-read.c, src/indexdb.c: Improved
	  autoconf checks and header files for mmap.

2003-10-22 13:10  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Fixed problem with
	  freeing memory.

2003-10-22 11:35  twu

	* segmentpos.c, src/segmentpos.c: Fixed small error with printing
	  accession bounds.

2003-10-22 11:34  twu

	* chrnum.c, iit-read.c, iit-read.h, iit-write.c, iit-write.h,
	  segmentpos.c, src/chrnum.c, src/iit-read.c, src/iit-read.h,
	  src/iit-write.c, src/iit-write.h, src/segmentpos.c, snap.c,
	  snapindex.c, src/gmap.c, src/gmapindex.c, src/snap.c,
	  src/snapindex.c: Fixed memory leaks.

2003-10-22 10:16  twu

	* acinclude.m4, block.h, chrnum.c, chrnum.h, config.h.in,
	  configure.ac, database.c, database.h, genomicpos.c, genomicpos.h,
	  get-genome.c, iit-read.c, iit-read.h, iit-write.c, iit-write.h,
	  config/acinclude.m4, src/Makefile.am, src/block.h, src/chrnum.c,
	  src/chrnum.h, src/genomicpos.c, src/genomicpos.h,
	  src/get-genome.c, src/iit-read.c, src/iit-read.h,
	  src/iit-write.c, src/iit-write.h, interval.c, interval.h,
	  match.c, match.h, offset.c, offset.h, offsetdb.c, offsetdb.h,
	  oligo.c, oligo.h, pair.c, pair.h, params.c, params.h,
	  segmentpos.c, segmentpos.h, sequence.c, snap.c, snapindex.c,
	  stage1.c, stage1.h, stage3.c, stage3.h, table.c, table.h,
	  src/gmap.c, src/gmapindex.c, src/interval.c, src/interval.h,
	  src/match.c, src/match.h, src/oligo.c, src/oligo.h, src/pair.c,
	  src/pair.h, src/params.c, src/params.h, src/segmentpos.c,
	  src/segmentpos.h, src/sequence.c, src/snap.c, src/snapindex.c,
	  src/stage1.c, src/stage1.h, src/stage3.c, src/stage3.h,
	  src/table.c, src/table.h: Eliminated dependence upon Berkeley DB.

2003-10-21 22:14  twu

	* table.c, table.h, src/table.c, src/table.h: Initial import into
	  CVS.

2003-10-21 16:05  twu

	* acinclude.m4, config/acinclude.m4, config.h.in, configure.ac,
	  genome.c, src/genome.c, genuncompress.c, src/genuncompress.c,
	  iit-read.c, src/iit-read.c, indexdb.c, src/indexdb.c: Added
	  checks for various mmap flags.

2003-10-21 15:59  twu

	* iitdef.h, src/iitdef.h: Restructed IIT_T commands.

2003-10-21 09:01  twu

	* iit-read.c, iit-read.h, iit-write.c, iit-write.h,
	  interval-read.c, interval-read.h, interval.c, interval.h, pair.c,
	  src/Makefile.am, src/iit-read.c, src/iit-read.h, src/iit-write.c,
	  src/iit-write.h, src/interval.c, src/interval.h, src/pair.c,
	  snap.c, src/gmap.c, src/snap.c: Restructured Interval_T and IIT_T
	  implementations so they don't depend on BerkeleyDB, and added
	  ability to write IITs.

2003-10-21 05:23  twu

	* database.c, acinclude.m4, config/acinclude.m4: Added provision
	  for BerkeleyDB version 4.1.

2003-10-21 05:21  twu

	* iit_store.c, src/iit_store.c: Changed format of input file to
	  have only intervals on the header line.

2003-10-21 05:10  twu

	* iit_get.c, src/iit_get.c: Changed program to use new IIT format.

2003-10-21 05:09  twu

	* iit_store.c, src/iit_store.c: Fixed problem with annotlist being
	  reversed.

2003-10-21 04:35  twu

	* iit_store.c, src/iit_store.c: Changed format of iit file to
	  include annotations.

2003-10-20 13:56  twu

	* sequence.c, src/sequence.c: Corrected type for return value of
	  fgetc.

2003-10-20 13:56  twu

	* oligo.c, src/oligo.c: Corrected type for return value of
	  Reader_getc.

2003-10-20 10:49  twu

	* stage1.h, src/stage1.h: Removed db.h as an included header.

2003-10-20 10:49  twu

	* acinclude.m4, config/acinclude.m4: Added -rpath flag during
	  linking of Berkeley DB.

2003-10-20 08:45  twu

	* configure, Makefile.in: Removing from CVS.

2003-10-20 08:44  twu

	* Makefile.in, configure: Result of autoreconf.

2003-10-20 08:43  twu

	* src/Makefile.am: Added header files to SOURCES.

2003-10-20 08:43  twu

	* configure.ac: Added no-dependencies option.

2003-10-20 06:17  twu

	* iit-read.c, src/iit-read.c: Removed MAP_VARIABLE from mmap call,
	  because not recognized by Linux.

2003-10-20 06:07  twu

	* Makefile.in: Added various auxiliary files.

2003-10-20 06:07  twu

	* sequence.c, src/sequence.c: Renamed variable strlen to avoid
	  compiler error on Linux.

2003-10-20 05:44  twu

	* depcomp, compile, Makefile.in, config.guess, config.sub: Initial
	  import into CVS.

2003-10-20 05:27  twu

	* Makefile.in: Initial import into CVS.

2003-10-20 05:26  twu

	* missing, config/missing, mkinstalldirs, config/mkinstalldirs:
	  Provided updated version.

2003-10-20 05:24  twu

	* configure, install-sh, config/install-sh: Initial import into
	  CVS.

2003-10-20 05:15  twu

	* genome.c, genomicpos.c, iit-read.c, iit-read.h, indexdb.c,
	  intlist.c, intlist.h, match.c, md5.c, mem.c, offset.c,
	  offsetdb.c, oligoindex.c, src/Makefile.am, src/genome.c,
	  src/genomicpos.c, src/iit-read.c, src/iit-read.h, src/indexdb.c,
	  src/intlist.c, src/intlist.h, src/match.c, src/md5.c, src/mem.c,
	  src/oligoindex.c, pair.c, segmentpos.c, segmentpos.h, uintlist.c,
	  uintlist.h, src/pair.c, src/segmentpos.c, src/segmentpos.h,
	  src/uintlist.c, src/uintlist.h: Addressed compiler warnings from
	  gcc.

2003-10-18 23:40  twu

	* acinclude.m4, config/acinclude.m4, src/Makefile.am, blackboard.c,
	  configure.ac, reqpost.c, snap.c, src/blackboard.c, src/gmap.c,
	  src/reqpost.c, src/snap.c: Allowed pthreads to be enabled or
	  disabled.

2003-10-18 13:11  twu

	* assert.c, src/assert.c, block.c, chrnum.c, complement.c,
	  src/block.c, src/chrnum.c, src/complement.c, database.c,
	  dynprog.c, src/dynprog.c, except.c, genome.c, genomicpos.c,
	  genuncompress.c, src/except.c, src/genome.c, src/genomicpos.c,
	  src/genuncompress.c, get-genome.c, iit-read.c, src/get-genome.c,
	  src/iit-read.c, indexdb.c, src/indexdb.c, interval-read.c,
	  intron.c, list.c, src/intron.c, src/list.c, longoligomer.c,
	  match.c, src/match.c, matchpair.c, src/matchpair.c, md5.c,
	  src/md5.c, offset.c, offsetdb.c, oligo.c, oligoindex.c,
	  src/oligo.c, src/oligoindex.c, pair.c, src/pair.c, pairpool.c,
	  src/pairpool.c, params.c, src/params.c, reader.c, src/reader.c,
	  reqpost.c, request.c, src/reqpost.c, src/request.c, result.c,
	  segmentpos.c, sequence.c, snap.c, snapindex.c, stage1.c,
	  stage2.c, stage3.c, src/gmap.c, src/gmapindex.c, src/result.c,
	  src/segmentpos.c, src/sequence.c, src/snap.c, src/snapindex.c,
	  src/stage1.c, src/stage2.c, src/stage3.c, stopwatch.c,
	  src/stopwatch.c: Added RCS Id string correctly

2003-10-18 13:07  twu

	* assert.c, src/assert.c: Added RCS Id string correctly

2003-10-18 12:17  twu

	* assert.c, src/assert.c, block.c, src/block.c, chrnum.c,
	  src/chrnum.c, complement.c, src/complement.c, database.c,
	  dynprog.c, src/dynprog.c, except.c, src/except.c, genome.c,
	  src/genome.c, genomicpos.c, src/genomicpos.c, genuncompress.c,
	  src/genuncompress.c, get-genome.c, src/get-genome.c, iit-read.c,
	  indexdb.c, src/iit-read.c, src/indexdb.c, interval-read.c,
	  intron.c, src/intron.c, list.c, src/list.c, longoligomer.c,
	  match.c, src/match.c, matchpair.c, src/matchpair.c, md5.c,
	  src/md5.c, offset.c, offsetdb.c, oligo.c, oligoindex.c,
	  src/oligo.c, src/oligoindex.c, pair.c, pairpool.c, params.c,
	  reader.c, reqpost.c, request.c, result.c, segmentpos.c,
	  sequence.c, snap.c, snapindex.c, stage1.c, src/gmap.c,
	  src/gmapindex.c, src/pair.c, src/pairpool.c, src/params.c,
	  src/reader.c, src/reqpost.c, src/request.c, src/result.c,
	  src/segmentpos.c, src/sequence.c, src/snap.c, src/snapindex.c,
	  src/stage1.c, stage2.c, stage3.c, stopwatch.c, src/stage2.c,
	  src/stage3.c, src/stopwatch.c: Added rcsid strings.

2003-10-18 03:10  twu

	* blackboard.c, src/blackboard.c, block.c, src/block.c,
	  complement.c, src/complement.c, database.c, dynprog.c,
	  src/dynprog.c, except.c, src/except.c, iit-read.c,
	  src/iit-read.c, interval-read.c, intron.c, src/intron.c, list.c,
	  src/list.c, matchpair.c, src/matchpair.c, md5.c, src/md5.c,
	  mem.c, src/mem.c, mem.h, src/mem.h, oligo.c, src/oligo.c,
	  oligoindex.c, src/oligoindex.c, pair.c, src/pair.c, pairpool.c,
	  src/pairpool.c, params.c, src/params.c, reader.c, src/reader.c,
	  reqpost.c, request.c, src/reqpost.c, src/request.c, result.c,
	  sequence.c, stage2.c, stopwatch.c, src/result.c, src/sequence.c,
	  src/stage2.c, src/stopwatch.c: Rearranged header includes.

2003-10-18 01:56  twu

	* mem.c, src/mem.c, blackboard.c, src/blackboard.c: Rearranged
	  header includes.

2003-10-18 01:51  twu

	* longoligomer.h: Defined T for both cases of HAVE_64_BIT.

2003-10-18 01:50  twu

	* longoligomer.c: Added conditional compiling based on HAVE_64_BIT.

2003-10-18 01:49  twu

	* offset.h: Added necessary header file stdio.h.

2003-10-18 01:49  twu

	* types.h, src/types.h: Added compiler directives from config.h.

2003-10-18 01:48  twu

	* configure.ac: Initial changes to configure.scan to make autoconf
	  and automake work for the cc compiler.

2003-10-18 01:47  twu

	* Makefile: Removed Makefile from CVS, because it is now generated
	  from Makefile.am by automake, and then from Makefile.in by
	  configure.

2003-10-18 01:43  twu

	* config.h.in, acinclude.m4, config/acinclude.m4, src/Makefile.am,
	  AUTHORS, COPYING, INSTALL, NEWS, README, ChangeLog,
	  mkinstalldirs, config/mkinstalldirs, missing, config/missing:
	  Added files for autoconf and automake to work.

2003-10-18 01:39  twu

	* configure.ac: Initial configure.ac from configure.scan produced
	  by autoscan.

2003-10-17 05:34  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c, gencompress.c:
	  Moved gencompress function inside snapindex (previously in
	  gencompress.c).

2003-10-17 02:22  twu

	* segmentpos.c, src/segmentpos.c: Changed type of relstart and
	  relend to int, due to problems with long.

2003-10-16 07:55  twu

	* dynprog.c, src/dynprog.c: Removed splice-site.c.

2003-10-16 07:54  twu

	* commafmt.c, commafmt.h, genomicpos.c, genomicpos.h, match.c,
	  pair.c, segmentpos.c, src/genomicpos.c, src/genomicpos.h,
	  src/match.c, src/pair.c, src/segmentpos.c: Moved commafmt command
	  to genomicpos.c.

2003-10-16 06:49  twu

	* types.h, src/types.h: Defined UINT8 only if HAVE_64_BIT is
	  defined.

2003-10-16 06:48  twu

	* splice-site.c, splice-site.h: Removed splice-site.c from CVS.

2003-10-16 06:45  twu

	* readcirc.c, readcirc.h: Removing readcirc from CVS.

2003-10-16 06:45  twu

	* radixsort.c, radixsort.h: Removing radixsort from CVS.

2003-10-16 06:42  twu

	* boyer-moore.c, boyer-moore.h: Removed Boyer-Moore procedures from
	  CVS.

2003-10-16 06:41  twu

	* longoligomer.h: Introduced constants and procedures for
	  Longoligomer_T on 32-bit systems.

2003-10-16 06:40  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Changed output
	  type of write_genome_file.

2003-10-16 06:40  twu

	* indexdb.c, src/indexdb.c, indexdb.h, src/indexdb.h: Introduced
	  Storedoligomer_T.

2003-10-16 06:39  twu

	* iit-read.c, src/iit-read.c: Added type cast from void * to char
	  *.

2003-10-16 06:39  twu

	* oligo.c, src/oligo.c, oligo.h, src/oligo.h: Created 32-bit
	  versions of procedures.

2003-10-16 06:38  twu

	* match.c, src/match.c: Removed functions Match_print() and
	  oligo_nt().

2003-10-16 06:38  twu

	* stage1.c, src/stage1.c: Removed mask from Block_T.  Removed
	  function Match_print().

2003-10-16 06:37  twu

	* block.c, src/block.c, block.h, src/block.h: Removed mask from
	  Block_T.

2003-10-16 06:36  twu

	* longoligomer.c: Added object Longoligomer_T for 32-bit systems.

2003-10-13 07:58  twu

	* Makefile, chrnum.c, database.c, gencompress.c, genome.c,
	  genome.h, genuncompress.c, stage1.c, src/chrnum.c, src/genome.c,
	  src/genome.h, src/genuncompress.c, src/stage1.c: Changed unsigned
	  int to more descriptive types.

2003-10-13 07:58  twu

	* genomicpos.c, genomicpos.h, longoligomer.h, shortoligomer.h,
	  src/genomicpos.c, src/genomicpos.h, src/shortoligomer.h: Added
	  new types.

2003-10-13 07:36  twu

	* chrnum.c, chrnum.h, match.c, match.h, offset.c, offset.h,
	  src/chrnum.c, src/chrnum.h, src/match.c, src/match.h, pair.c,
	  pair.h, segmentpos.c, segmentpos.h, snap.c, snapindex.c,
	  stage1.c, stage3.c, stage3.h, src/gmap.c, src/gmapindex.c,
	  src/pair.c, src/pair.h, src/segmentpos.c, src/segmentpos.h,
	  src/snap.c, src/snapindex.c, src/stage1.c, src/stage3.c,
	  src/stage3.h: Changed unsigned int to more descriptive types.

2003-10-13 07:10  twu

	* offsetdb.c, offsetdb.h: Added type for Chrnum_T.  Removed
	  function Offset_position_to_chr.

2003-10-13 06:40  twu

	* oligoindex.c, stage1.c, stage2.c, src/oligoindex.c, src/stage1.c,
	  src/stage2.c: Changed unsigned long and unsigned int to more
	  descriptive types.

2003-10-13 06:37  twu

	* add-chrpos-to-endpoints.c: Removed file used for prototyping.

2003-10-13 06:28  twu

	* rsort-check.c, rsort-test.c: Removed utility files for radixsort.

2003-10-13 06:27  twu

	* sequence.c, src/sequence.c: Removed code for computing CRC32
	  checksum.

2003-10-13 06:24  twu

	* sample-oligos.c: Removed sample-oligos.c, which was used for
	  prototyping.

2003-10-13 06:15  twu

	* block.c, block.h, indexdb.c, indexdb.h, match.c, match.h,
	  oligo.c, oligo.h, oligoindex.c, oligoindex.h, src/block.c,
	  src/block.h, src/indexdb.c, src/indexdb.h, src/match.c,
	  src/match.h, src/oligo.c, src/oligo.h, src/oligoindex.c,
	  src/oligoindex.h: Changed unsigned long and unsigned int to more
	  informative types.

2003-10-13 06:15  twu

	* Makefile: Removed cksum-fa

2003-10-13 06:15  twu

	* prb.c, prb.h: Removed prb.c and prb.h, which implemented
	  red-black trees.

2003-10-13 05:19  twu

	* cksum.c: Removed cksum.c, which is now computed in sequence.c

2003-10-13 05:18  twu

	* cksum-fa.c: Removed cksum-fa.c, which was a utility program.

2003-10-13 05:16  twu

	* cell.c, cell.h: Removed Cell_T, which was designed for the HashDB
	  storage scheme for genomic oligomers.

2003-10-13 05:03  twu

	* pair.c, src/pair.c, pair.h, src/pair.h, sequence.c,
	  src/sequence.c, sequence.h, src/sequence.h, stage3.c,
	  src/stage3.c: Added provision for correcting coverage in the
	  presence of genomic gaps at the ends.

2003-10-13 05:03  twu

	* chrnum.c, src/chrnum.c: Fixed a bug in printing output.

2003-10-09 06:31  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h: Added reward for
	  spliced cDNAs based on number of exons, if it's greater than 2.
	  Also, added flag for conservative behavior for splice site
	  prediction, by reducing the reward for canonical splice sites.
	  Note, however, that such behavior causes SNAP to perform poorly
	  in the presence of sequence errors.

2003-10-09 06:30  twu

	* dynprog.c, src/dynprog.c, dynprog.h, src/dynprog.h, params.c,
	  src/params.c, params.h, src/params.h, snap.c, src/gmap.c,
	  src/snap.c: Added flag for conservative behavior for splice site
	  prediction, by reducing the reward for canonical splice sites.
	  Note, however, that such behavior causes SNAP to perform poorly
	  in the presence of sequence errors.

2003-10-07 09:30  twu

	* iit-read.c, src/iit-read.c: Adapt to new format of bounds
	  database contents.

2003-10-07 09:30  twu

	* pair.c, src/pair.c: Makes correct call to IIT_get when
	  coordinates are in reverse order.

2003-08-19 10:42  twu

	* iit.c, iit.h, interval.c, interval.h, src/interval.c,
	  src/interval.h, Makefile, iit-read.c, interval-read.c, pair.h,
	  params.h, snap.c, stage3.h, src/gmap.c, src/iit-read.c,
	  src/pair.h, src/params.h, src/snap.c, src/stage3.h: Changed
	  filenames from iit.c and interval.c to iit-read.c and
	  interval-read.c

2003-08-19 10:40  twu

	* whats_on, util/whats_on: Generalized procedure for identifying
	  FASTA files containing ESTs.

2003-08-19 10:39  twu

	* sequence.c, src/sequence.c: Fixed conversion of char to unsigned
	  char.

2003-08-19 10:37  twu

	* snap.c, src/gmap.c, src/snap.c, stage3.c, src/stage3.c, stage3.h,
	  src/stage3.h, params.c, src/params.c, params.h, src/params.h,
	  pair.c, src/pair.c, pair.h, src/pair.h, iit-read.c, iit.c,
	  src/iit-read.c, iit-read.h, iit.h, src/iit-read.h,
	  interval-read.c, interval.c, src/interval.c, interval-read.h,
	  interval.h, src/interval.h, bounds.c, bounds.h, Makefile: Changed
	  calls to iit to open the files just once.

2003-08-19 10:02  twu

	* bounds.c, bounds.h: Adding bounds.c file to compute bounds.

2003-08-19 05:57  twu

	* iit-read.c, iit.c, src/iit-read.c, database.c, database.h,
	  Makefile: Added ability to use a gene bounds iit file.

2003-08-19 05:57  twu

	* interval-read.c, interval.c, src/interval.c, interval-read.h,
	  interval.h, src/interval.h: Revised version from berkeleydb CVS
	  repository.

2003-08-19 05:56  twu

	* snap.c, src/gmap.c, src/snap.c, stage3.c, src/stage3.c, stage3.h,
	  src/stage3.h, params.c, src/params.c, params.h, src/params.h,
	  pair.c, src/pair.c, pair.h, src/pair.h: Added capability to use a
	  gene bounds iit file.

2003-08-18 07:20  twu

	* iit-read.h, iit.h, src/iit-read.h: Initial import into CVS.

2003-08-18 07:10  twu

	* iit_get.c, src/iit_get.c: Compare only to query length.

2003-08-18 06:17  twu

	* get-genome.c, src/get-genome.c: Fixes procedure isrange to make a
	  copy of the string.

2003-07-07 08:25  twu

	* whats_on, util/whats_on: Changed behavior to not die if directory
	  isn't found.

2003-07-07 08:25  twu

	* segmentpos.c, src/segmentpos.c: Fixed sorting and printing for
	  chromosomes like 2L.

2003-07-07 08:24  twu

	* stage3.h, src/stage3.h: Removed Stage3_goodness as an external
	  procedure.

2003-07-07 08:24  twu

	* stage3.c, src/stage3.c: Changed goodness within a given
	  chromosomal segment to include canonical introns, but goodness
	  between chromosomal segments to exclude this.

2003-07-07 08:22  twu

	* stage2.c, src/stage2.c: Increased MAXHITS from 20 to 1000.
	  Previous value was too low and led to splicing errors.

2003-07-07 08:22  twu

	* get-genome.c, src/get-genome.c: Changed program to try segment
	  first as a chromosome, then as a contig.

2003-07-07 08:21  twu

	* offsetdb.c: Improved output statements to print beginning and
	  ending of chromosomes.

2003-07-07 08:20  twu

	* chrnum.c, src/chrnum.c, chrnum.h, src/chrnum.h: Fixed sorting and
	  printing for chromosomes like 2L.

2003-06-19 09:27  twu

	* dynprog.c, src/dynprog.c: Changed penalties.	Made reward for
	  extension multiplicative.

2003-06-19 09:27  twu

	* stage3.c, src/stage3.c: Added debugging statements for
	  finalscore.

2003-06-19 09:26  twu

	* cksum-fa.c: Added comments.

2003-06-19 09:25  twu

	* md5.c, md5.h, md5.t.c, src/md5.c, src/md5.h, src/md5.t.c,
	  types.h, src/types.h, Makefile, snap.c, src/gmap.c, src/snap.c,
	  snap_compress.pl, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/snap_compress.pl,
	  snap_uncompress.pl, util/gmap_uncompress.pl,
	  util/gmap_uncompress.pl.in, util/snap_uncompress.pl, sequence.c,
	  src/sequence.c, sequence.h, src/sequence.h, params.c,
	  src/params.c, params.h, src/params.h: Added MD5 calculations.

2003-06-17 05:51  twu

	* Makefile: Rearranged lines.

2003-06-17 05:51  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed calculation of indexdb to
	  occur only once for user-provided segment.

2003-06-17 05:51  twu

	* sequence.c, src/sequence.c, sequence.h, src/sequence.h: Added
	  computation for crc32.

2003-06-13 08:14  twu

	* dynprog.c, src/dynprog.c: Changed reward for partial match to be
	  zero.

2003-06-13 08:13  twu

	* stage3.c, src/stage3.c: Fixed bug where pairs_fwd or pairs_rev
	  might be NULL.

2003-06-03 05:40  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h: Created separate
	  paths for forward and revcomp directions after smoothing.  Added
	  back intron score during calculations.

2003-06-03 05:39  twu

	* stage3.c, src/stage3.c: Separated calculations of forward and
	  revcomp paths.

2003-06-03 05:39  twu

	* snap.c, src/gmap.c, src/snap.c: Increased size of maxlookback.

2003-06-03 05:37  twu

	* pair.c, src/pair.c, pair.h, src/pair.h: Added calculation of
	  number of canonical exons.

2003-06-03 05:37  twu

	* dynprog.c, src/dynprog.c: Setting finalscore as a return value.

2003-06-03 04:42  twu

	* stage3.c, src/stage3.c: Added number of canonical exons to
	  goodness criterion.  Added "Stage 3" to debug statements.

2003-05-27 07:43  twu

	* pair.c, src/pair.c, pair.h, src/pair.h: Changed Pair_fracidentity
	  to work on a list, rather than an array.

2003-05-27 07:42  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h, stage2.c,
	  src/stage2.c, stage2.h, src/stage2.h, snap.c, src/gmap.c,
	  src/snap.c: Moved alignment of different cDNA direction from
	  stage 2 to stage 3.

2003-05-22 10:30  twu

	* stage3.c, src/stage3.c: Changed goodness function to ignore
	  number of canonical introns.

2003-05-22 10:30  twu

	* snap.c, src/gmap.c, src/snap.c: Added parameter for sufflookback,
	  potentially different from maxlookback, but found that setting
	  maxlookback >> sufflookback led to long, poor alignments, so set
	  maxlookback = sufflookback.

2003-05-22 10:28  twu

	* params.c, src/params.c, params.h, src/params.h, stage2.c,
	  src/stage2.c, stage2.h, src/stage2.h: Added separate parameter
	  for sufflookback, to be used in stage 2, and possibly different
	  from maxlookback, used in stage 3.

2003-05-03 14:04  twu

	* genome.c, genuncompress.c, iit-read.c, iit.c, indexdb.c,
	  src/genome.c, src/genuncompress.c, src/iit-read.c, src/indexdb.c:
	  Removed MAP_VARIABLE from mmap command, because it is not
	  available in Linux.

2003-05-03 14:02  twu

	* hashdb-read.c, hashdb-read.h, hashdb-write.c, hashdb-write.h,
	  hashdb.c, hashdb.h, hash-test.c: Removed hashdb files, which have
	  been replaced by indexdb.

2003-05-03 14:00  twu

	* whats_on, util/whats_on: Added error message.

2003-05-03 13:59  twu

	* Makefile: Removed old Makefile commands.

2003-05-03 13:59  twu

	* snapgenerate.c, snapindex.c, src/gmapindex.c, src/snapindex.c:
	  Moved functions from snapgenerate.c to snapindex.c, so only
	  snapindex is needed to create SNAP genome files.

2003-05-03 13:55  twu

	* genuncompress.c, src/genuncompress.c: Initial import into CVS.

2003-04-30 10:46  twu

	* stage2.c, src/stage2.c: Added check for MAXHITS in stage 2, to
	  prevent slowness problems from repetitive cDNAs in repetitive
	  genomic segments (such as AA704019).

2003-04-30 10:45  twu

	* stage1.c, src/stage1.c: Added debugging statement.

2003-04-30 10:45  twu

	* snap_uncompress.pl, util/gmap_uncompress.pl,
	  util/gmap_uncompress.pl.in, util/snap_uncompress.pl: Fixed
	  problem where gpos was not handled correctly for the minus
	  strand.

2003-04-30 10:42  twu

	* chrnum.c, src/chrnum.c: Fixed problem where signed chromosomes
	  were being printed incorrectly.

2003-04-29 00:28  twu

	* whats_on, util/whats_on: Fixed problem where genomic coordinates
	  were in the order of largest, then smallest (reverse strand).

2003-04-27 02:33  twu

	* stage3.c, src/stage3.c: Removed queryoffset.

2003-04-27 02:32  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h: Removed
	  queryoffset.	Made sampling interval variable.  Added bounding of
	  a querypos to a single hit if its top score exceeds its second
	  highest score.

2003-04-27 02:30  twu

	* snap.c, src/gmap.c, src/snap.c: Changed lookback and
	  extramaterial_paired.

2003-04-27 02:12  twu

	* sequence.c, src/sequence.c: Changed trimming to leave
	  non-poly-A/T oligomers.

2003-04-27 02:11  twu

	* offsetdb.c: Extra blank line.

2003-04-27 02:09  twu

	* chrnum.c, src/chrnum.c, database.c, get-genome.c,
	  src/get-genome.c, segmentpos.c, src/segmentpos.c: Changed
	  interpretation of chromosome numbers to allow all single letters
	  and all numbers.

2003-04-16 10:49  twu

	* accpos.c, Makefile: Removed file accpos.c, which isn't being used
	  anymore.

2003-04-16 06:06  twu

	* sequence.c, src/sequence.c, sequence.h, src/sequence.h, genome.c,
	  src/genome.c: Removed offset as a parameter for
	  Sequence_genomic_new.

2003-04-16 06:05  twu

	* mem.c, src/mem.c: Removed upper limit check on allocating memory.

2003-04-16 05:50  twu

	* pair.h, src/pair.h: Removed queryoffset from print routines.

2003-04-16 05:49  twu

	* pair.c, src/pair.c: Removed queryoffset from print routines.
	  Fixed calculation of genomic distances for Crick strand.

2003-04-07 03:24  twu

	* dynprog.c, src/dynprog.c: Reduced rewards for canonical introns.

2003-04-07 03:24  twu

	* pair.c, src/pair.c: Added conversion to uppercase.

2003-04-07 03:24  twu

	* mem.c, src/mem.c: Added check for unexpectedly large allocations.

2003-04-01 23:44  twu

	* stage3.c, src/stage3.c: Made separate procedures for 3' and 5'
	  ends.  Turned off Boyer-Moore extension at ends.  Added checks to
	  prevent dynamic programming past end of sequence.

2003-04-01 23:43  twu

	* params.c, src/params.c: Removed freeing of version.

2003-04-01 23:37  twu

	* pairpool.c, src/pairpool.c: Added additional debugging checks.

2003-04-01 23:36  twu

	* pair.c, src/pair.c: Improved output for user-provided segments.

2003-04-01 23:34  twu

	* sequence.c, src/sequence.c, sequence.h, src/sequence.h, match.c,
	  src/match.c, matchpair.c, src/matchpair.c, matchpair.h,
	  src/matchpair.h, offset.c: Now performing stage 1 on
	  user-provided segments.  This eliminates poor alignments when the
	  user-provided segment is longer than stage 1 would have provided.

2003-04-01 23:34  twu

	* segmentpos.c, src/segmentpos.c: Added limit to number of
	  accessions reported.

2003-04-01 23:33  twu

	* request.c, src/request.c, request.h, src/request.h: Changed from
	  name from genomicseg to usersegment.

2003-04-01 23:33  twu

	* stage1.c, src/stage1.c: Removed offset from call to Block_T
	  procedures.

2003-04-01 23:31  twu

	* indexdb.c, src/indexdb.c, indexdb.h, src/indexdb.h, snap.c,
	  src/gmap.c, src/snap.c: Now performing stage 1 on user-provided
	  segments.  This eliminates poor alignments when the user-provided
	  segment is longer than stage 1 would have provided.

2003-04-01 23:29  twu

	* genome.c, src/genome.c: Renamed some procedures.

2003-04-01 23:28  twu

	* dynprog.c, src/dynprog.c: Increased penalties for mismatch.

2003-04-01 23:28  twu

	* chrnum.c, src/chrnum.c: Allowed chromosome 0.

2003-04-01 23:28  twu

	* block.c, src/block.c, block.h, src/block.h: Removed offset from
	  list of parameters.

2003-04-01 23:27  twu

	* blackboard.c, src/blackboard.c, blackboard.h, src/blackboard.h:
	  Changed from name from genomicseg to usersegment.

2003-03-27 05:22  twu

	* stage3.c, src/stage3.c, pair.c, src/pair.c, snap_compress.pl,
	  util/gmap_compress.pl, util/gmap_compress.pl.in,
	  util/snap_compress.pl, snap_uncompress.pl,
	  util/gmap_uncompress.pl, util/gmap_uncompress.pl.in,
	  util/snap_uncompress.pl: Changed alignment output for dual
	  breaks.

2003-03-24 16:30  twu

	* dynprog.c, src/dynprog.c: Created an inline procedure and scheme
	  for scoring canonical and alternate introns.	Increased penalties
	  for mismatches.

2003-03-24 16:26  twu

	* intron.c, src/intron.c, intron.h, src/intron.h: Moved most
	  functions to other files, to increase speed.

2003-03-24 16:24  twu

	* stage3.c, src/stage3.c, pair.c, src/pair.c, pair.h, src/pair.h,
	  pairdef.h, src/pairdef.h, pairpool.c, src/pairpool.c: Added field
	  to Pair_T object to denote a gap.

2003-03-24 16:23  twu

	* sequence.c, src/sequence.c: Fixed bug that caused large amounts
	  of memory to be allocated.

2003-03-24 09:46  twu

	* snap_compress.pl, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/snap_compress.pl: Introduced a
	  better error statement.

2003-03-24 09:46  twu

	* stage2.c, src/stage2.c: Changed sampling to start at -1 after the
	  first 8-mer missed, and then go back by the Nyquest rate.

2003-03-24 09:45  twu

	* stage3.c, src/stage3.c: Introduced peelback for single gaps.

2003-03-21 06:24  twu

	* genome.c, pair.c, pair.h, sequence.c, src/genome.c, src/pair.c,
	  src/pair.h, src/sequence.c, sequence.h, snap.c, stage3.c,
	  src/gmap.c, src/sequence.h, src/snap.c, src/stage3.c: Fixed
	  algorithm to handle poly-T starts as well as poly-A ends.  Added
	  extra information to Sequence_T structure and output procedures
	  to handle this correctly.

2003-03-21 02:37  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed problems with Stage3_T
	  objects that were not assigned to NULL.  Added flushing of output
	  for debugging.

2003-03-21 02:36  twu

	* dynprog.c, src/dynprog.c: Fixed dynamic programming on ends so
	  the genomic segment won't stick out.

2003-03-20 02:25  twu

	* spidey_compress.pl, util/spidey_compress.pl: Modified routine to
	  look for spaces of at least 10, instead of 20.

2003-03-20 02:24  twu

	* dynprog.c, src/dynprog.c: Added a separate reward for canonical
	  introns, depending on the defect rate.

2003-03-20 02:23  twu

	* list.c, src/list.c, list.h, src/list.h: Added a command for
	  setting the head of a list.

2003-03-20 02:23  twu

	* pair.c, src/pair.c: Fixed counting of indels.

2003-03-20 02:23  twu

	* pairpool.c, src/pairpool.c: Created new debugging commands.

2003-03-20 02:22  twu

	* snap.c, src/gmap.c, src/snap.c: Added trimming of first or last
	  exon in stage 2 if the defect rate is high enough and the exons
	  are too long.  Increased lookback from 60 to 90.

2003-03-20 02:21  twu

	* stage3.c, src/stage3.c: Modified peelback to go past
	  nonconsecutive hits, stopping only at an intron.

2003-03-20 02:20  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h: Added trimming of
	  first or last exon if the defect rate is high enough and the
	  exons are too long.

2003-03-16 06:47  twu

	* stage2.c, src/stage2.c: Added hooks for making smooth_path depend
	  on defect_rate, but this appears to be a bad idea.

2003-03-16 06:46  twu

	* pair.c, src/pair.c: Improved consistency check to work when
	  cdna_direction is initially zero.

2003-03-16 06:45  twu

	* dynprog.c, src/dynprog.c, dynprog.h, src/dynprog.h, stage3.c,
	  src/stage3.c: Changed effect of defect rate to be on mismatches
	  and gaps, rather than intron scores.

2003-03-14 22:48  twu

	* pair.c, pair.h, snap.c, stage2.c, stage2.h, stage3.c, src/gmap.c,
	  src/pair.c, src/pair.h, src/snap.c, src/stage2.c, src/stage2.h,
	  src/stage3.c, stage3.h, src/stage3.h: Added check for consistency
	  of intron directions, and ability to back track to stage 2 with
	  forced cdna_directions if the stage 3 result is inconsistent.

2003-03-14 09:17  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h, stage3.c,
	  src/stage3.c, pair.c, src/pair.c, pair.h, src/pair.h, dynprog.c,
	  src/dynprog.c, dynprog.h, src/dynprog.h: Added estimation of
	  defect_rate in stage 2, and used it to change parameters in
	  dynamic programming and extension of ends.

2003-03-12 14:21  twu

	* stage3.c, src/stage3.c: Changed limitation on Boyer-Moore search
	  to be a certain number of hits.  This compensates for the fact
	  that smaller oligomers will occur more frequently than longer
	  ones, and that longer ones are more statistically significant.

2003-03-12 00:44  twu

	* stage3.h, src/stage3.h, stage3.c, src/stage3.c: Limited length of
	  Boyer-Moore search at ends.  Changed name of minendsearch to
	  minendtrigger.

2003-03-12 00:43  twu

	* snap.c, src/gmap.c, src/snap.c, params.c, src/params.c, params.h,
	  src/params.h: Changed name of minendsearch to minendtrigger.

2003-03-11 07:13  twu

	* dynprog.c, src/dynprog.c: Extended the search range of
	  bridge_gap, so that it finds introns even at the bounds of the
	  dynamic programming.

2003-03-11 04:36  twu

	* params.c, src/params.c, params.h, src/params.h, snap.c,
	  src/gmap.c, src/snap.c, stage3.c, src/stage3.c, stage3.h,
	  src/stage3.h: Added parameter for minendsearch.

2003-03-11 04:35  twu

	* dynprog.c, src/dynprog.c: Fixed safety check in intron_score for
	  reading off end of segment.

2003-03-11 04:17  twu

	* stage3.c, src/stage3.c: Rearranged computation of stage 3, such
	  that middle is computed first, then cDNA direction is recomputed,
	  then 5' and 3' ends are computed.

2003-03-11 04:16  twu

	* pair.c, src/pair.c, pair.h, src/pair.h: Added function for
	  computing cDNA direction from list of pairs.

2003-03-11 04:15  twu

	* dynprog.c, src/dynprog.c: Adjusted various dynamic programming
	  scores.  Fixed coordinates in gap.  Added check for very short
	  introns.

2003-03-11 02:44  twu

	* stage3.c, src/stage3.c: Discrimination between paired gap dynamic
	  programming at ends and in middle.

2003-03-11 02:43  twu

	* dynprog.c, src/dynprog.c, dynprog.h, src/dynprog.h: Major rewrite
	  of dynamic programming procedures.  Changed from Gotoh algorithm
	  to pure banded procedure.  Reversing sequences when necessary, so
	  all computations are symmetric.

2003-03-10 09:47  twu

	* sim4_compress.pl, util/sim4_compress.pl, spidey_compress.pl,
	  util/spidey_compress.pl: Added output of the number of exons.

2003-03-10 09:47  twu

	* stage3.c, src/stage3.c: Added check for genomejump being zero or
	  negative, which would give rise to a position beyond the genomic
	  segment.

2003-03-10 09:46  twu

	* pair.c, src/pair.c: Added check for zero denominator.

2003-03-10 09:45  twu

	* boyer-moore.c: Added check for sequence to consist entirely of
	  valid nucleotides.

2003-03-09 03:24  twu

	* spidey_compress.pl, util/spidey_compress.pl: Added printing of
	  exon lengths, intron lengths, and dinucleotides, to match new
	  output of snap_compress.pl.  Fixed problems with parsing Spidey
	  output.

2003-03-09 03:23  twu

	* sim4_compress.pl, util/sim4_compress.pl: Added printing of exon
	  lengths, intron lengths, and dinucleotides, to match new output
	  of snap_compress.pl.

2003-03-09 03:23  twu

	* snap_compress.pl, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/snap_compress.pl: Fixed problem
	  when reverse intron is GT-AG.

2003-03-09 03:22  twu

	* snap_uncompress.pl, util/gmap_uncompress.pl,
	  util/gmap_uncompress.pl.in, util/snap_uncompress.pl: Fixed bug
	  that occurs when snap was called with -N, without printing intron
	  lengths.

2003-03-08 11:11  twu

	* stage1.c, src/stage1.c: Fixed a memory leak from not freeing
	  Stage1_T object.

2003-03-08 11:08  twu

	* block.c, src/block.c: Fixed bug which caused a memory leak
	  because we were overwriting a previous querypos.

2003-03-08 11:07  twu

	* oligo.c, src/oligo.c: Fixed debug message.

2003-03-07 01:49  twu

	* snap.c, src/gmap.c, src/snap.c: Reduced stage1size for short
	  query sequences (< 60 bp).

2003-03-07 01:48  twu

	* match.c, src/match.c, match.h, src/match.h, stage1.c,
	  src/stage1.c, stage1.h, src/stage1.h: Fixed Match_print to print
	  the correct oligo.

2003-03-07 01:47  twu

	* get-genome.c, src/get-genome.c: Changed header to contain the
	  version number.

2003-03-07 01:47  twu

	* snap_uncompress.pl, util/gmap_uncompress.pl,
	  util/gmap_uncompress.pl.in, util/snap_uncompress.pl: Added exon
	  lengths to compressed output.

2003-03-07 01:47  twu

	* snap_compress.pl, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/snap_compress.pl: Added exon
	  lengths to compressed output.  Removed printing of dinucleotides
	  for canonical introns.

2003-03-06 06:21  twu

	* stage3.c, src/stage3.c: Cleaned up code extensively.	Added
	  Boyer-Moore searches on both ends of cDNA.

2003-03-06 06:20  twu

	* dynprog.c, src/dynprog.c, dynprog.h, src/dynprog.h: Cleaned up
	  code by making separate procedures for single gap in middle, and
	  5' and 3' ends.

2003-03-06 06:18  twu

	* pair.c, src/pair.c, pair.h, src/pair.h: Added procedure for
	  dumping a list of pairs.

2003-03-06 06:18  twu

	* boyer-moore.c: Removed debugging statements.

2003-03-04 09:25  twu

	* Makefile, boyer-moore.c, boyer-moore.h: Addition of Boyer-Moore
	  string search.

2003-03-04 09:24  twu

	* stage3.c, src/stage3.c: Consolidated peelback code.  Beginning to
	  insert Boyer-Moore code.

2003-03-04 09:23  twu

	* stage2.c, src/stage2.c: Fixed bug where index was -1.

2003-03-04 08:43  twu

	* stage1.c, src/stage1.c, oligo.c, src/oligo.c, oligo.h,
	  src/oligo.h, block.c, src/block.c, block.h, src/block.h: Fixed
	  code to use stage1size instead of INDEX1PART in certain places.

2003-03-04 08:42  twu

	* snap_compress.pl, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/snap_compress.pl: Fixed code to
	  handle genomic accession when genomic sequence is provided by the
	  user.

2003-03-04 08:41  twu

	* pair.c, src/pair.c, sequence.c, src/sequence.c, sequence.h,
	  src/sequence.h, snap.c, src/gmap.c, src/snap.c: Fixed code to
	  print out genomic accession when genomic sequence is provided by
	  the user.

2003-03-04 08:41  twu

	* match.c, src/match.c: Fixed code to print just forward oligo.

2003-03-03 04:18  twu

	* intron.c, src/intron.c, pair.c, src/pair.c: Changed '===...==='
	  to represent a non-canonical intron.

2003-03-03 04:17  twu

	* dynprog.c, src/dynprog.c: Reduced reward to semi-canonical
	  introns to be slightly less than that for canonical introns.

2003-03-03 04:16  twu

	* stage3.c, src/stage3.c: Changed output of large gaps from
	  '=========' to '###...###'.

2003-03-03 04:16  twu

	* snap_uncompress.pl, util/gmap_uncompress.pl,
	  util/gmap_uncompress.pl.in, util/snap_uncompress.pl: Made changes
	  to accommodate enhancements to SNAP, namely use of '#' for large
	  gaps and switch of intronends and intronlengths info.

2003-03-03 04:15  twu

	* snap_compress.pl, util/gmap_compress.pl,
	  util/gmap_compress.pl.in, util/snap_compress.pl: Initial import
	  into CVS.

2003-03-02 11:56  twu

	* snap_uncompress.pl, util/gmap_uncompress.pl,
	  util/gmap_uncompress.pl.in, util/snap_uncompress.pl: Initial
	  import into CVS.

2003-03-02 02:10  twu

	* Makefile, dynprog.c, intron.c, intron.h, pair.c, splice-site.c,
	  src/dynprog.c, src/intron.c, src/intron.h, src/pair.c: Removed
	  use of splice site matrices and added identification of
	  semi-canonical dinucleotides.

2003-02-28 09:50  twu

	* params.c, src/params.c, params.h, src/params.h, stage3.c,
	  src/stage3.c, stage3.h, src/stage3.h, snap.c, src/gmap.c,
	  src/snap.c: Changed extramaterial at the end and for paired to be
	  parameters.

2003-02-28 09:49  twu

	* get-genome.c, src/get-genome.c: Changed program to check only
	  first four letters of genomic name.

2003-02-11 07:43  twu

	* pair.c, pair.h, stage3.c, src/pair.c, src/pair.h, src/stage3.c:
	  Adjusted goodness score of alignment by number of canonical
	  introns.

2003-02-11 07:23  twu

	* dynprog.c, dynprog.h, params.c, params.h, snap.c, src/dynprog.c,
	  src/dynprog.h, src/gmap.c, src/params.c, src/params.h,
	  src/snap.c, stage3.c, stage3.h, src/stage3.c, src/stage3.h:
	  Parameterized band size in dynamic programming and increased
	  bands for cross-species alignment.

2003-02-11 06:50  twu

	* oligoindex.c, oligoindex.h, params.c, params.h, snap.c, stage2.c,
	  stage3.c, stage3.h, src/gmap.c, src/oligoindex.c,
	  src/oligoindex.h, src/params.c, src/params.h, src/snap.c,
	  src/stage2.c, src/stage3.c, src/stage3.h: Parameterized INDEXSIZE
	  and made it different for cross-species alignment.

2003-02-11 06:22  twu

	* stage2.c, src/stage2.c: Added smooth_path step in stage 2 to
	  remove short spurious exon hits.

2003-02-03 07:59  twu

	* params.c, src/params.c, params.h, src/params.h: Replaced dbroot
	  with version.

2003-02-03 07:59  twu

	* snap.c, src/gmap.c, src/snap.c: Added reporting of version to
	  program.

2003-01-27 09:21  twu

	* stage3.c, src/stage3.c: Fixed problem where a base pair was
	  missed on the 5' end.

2003-01-27 09:21  twu

	* stage2.c, src/stage2.c: Fixed problems where genomic matches can
	  overlap.

2003-01-27 09:20  twu

	* pair.c, src/pair.c: Fixed problems in computing exon endpoints.

2003-01-22 05:55  twu

	* stage3.c, src/stage3.c: Reverted back to old method of building
	  pairs in the middle.

2003-01-22 05:52  twu

	* pair.c, src/pair.c: Added post-processing check for a gap at the
	  end of the alignment.

2003-01-22 05:52  twu

	* oligoindex.c, src/oligoindex.c: Added check for poly-T.

2003-01-03 06:36  twu

	* stage3.c, src/stage3.c: Made some changes to eliminate large gaps
	  at the 3' end.

2003-01-03 05:58  twu

	* snap.c, src/gmap.c, src/snap.c: Improved handling of case where
	  user provides both cDNA and genomic files.

2003-01-03 03:22  twu

	* stage3.c, src/stage3.c: Fixed bug when no pairs are found.

2003-01-03 03:20  twu

	* sequence.c, src/sequence.c: Fixed bug in failing to initialize.

2002-12-30 05:10  twu

	* params.c, src/params.c, params.h, src/params.h: Added parameter
	  for fwdonlyp.

2002-12-30 05:09  twu

	* pairpool.c, src/pairpool.c: Fixed small memory leak.

2002-12-30 03:41  twu

	* params.h, src/params.h: Changed genomeinvert from a bool to an
	  int.

2002-12-30 03:40  twu

	* pair.c, src/pair.c: Fixed bug where pointer was advanced before
	  freeing it.

2002-12-11 04:05  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed problem where complement
	  table was not initialized early enough.

2002-12-10 07:05  twu

	* sequence.c, src/sequence.c, sequence.h, src/sequence.h, snap.c,
	  src/gmap.c, src/snap.c: Improved procedure for trimming poly-A
	  tails.

2002-12-10 07:04  twu

	* pair.c, src/pair.c: Increased space for positions from 12 to 14.

2002-12-10 07:04  twu

	* complement.h, src/complement.h: Removed extraneous semicolon.

2002-12-10 07:03  twu

	* stage2.c, src/stage2.c: Fixed problem where no matching 8-mers
	  are found.

2002-12-04 02:24  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Write accession
	  names to .aux file, even if they do not start with NT_ or GA_.

2002-12-04 02:24  twu

	* snap.c, src/gmap.c, src/snap.c: Added routines for adding signs
	  to chromosomes, inverting the genome, printing intron lengths,
	  and trimming poly-A tails.

2002-12-04 02:23  twu

	* sequence.c, src/sequence.c, sequence.h, src/sequence.h: Added
	  routines for trimming poly-A tails.

2002-12-04 02:21  twu

	* pair.c, src/pair.c, pair.h, src/pair.h, params.c, src/params.c,
	  params.h, src/params.h, stage3.c, src/stage3.c, stage3.h,
	  src/stage3.h: Added routines for adding signs to chromosomes,
	  inverting the genome, and printing intron lengths.

2002-12-04 02:20  twu

	* chrnum.c, src/chrnum.c, chrnum.h, src/chrnum.h, match.c,
	  src/match.c: Added routines for adding signs to chromosomes.

2002-12-04 02:19  twu

	* Makefile, complement.c, complement.h, src/complement.c,
	  src/complement.h, genome.c, src/genome.c: Added files for
	  handling complements.

2002-11-25 22:19  twu

	* match.c, pair.c, src/match.c, src/pair.c: Changed printing of
	  FWD/REV to +/-.  Added printing of intron lengths.

2002-11-25 21:42  twu

	* pair.c, pair.h, params.c, params.h, snap.c, stage3.c, stage3.h,
	  src/gmap.c, src/pair.c, src/pair.h, src/params.c, src/params.h,
	  src/snap.c, src/stage3.c, src/stage3.h: Added ability to print
	  genome first in alignment.

2002-11-25 02:55  twu

	* snap.c, src/gmap.c, src/snap.c: Added iteration code for
	  cross-species alignments.

2002-11-25 02:54  twu

	* Makefile: Added an object Matchpair_T to hold pairs of Match_T
	  objects.

2002-11-25 02:54  twu

	* segmentpos.c, src/segmentpos.c: Added a check against freeing a
	  null value.

2002-11-25 02:53  twu

	* result.c, src/result.c, result.h, src/result.h: Created a
	  Stage1_T object that can hold state, for resuming stage 1
	  calculations later.

2002-11-25 02:53  twu

	* dynprog.c, src/dynprog.c: Changed allocation procedures for
	  Matrix_T and Directions_T.  Provided hooks for doing band-limited
	  memory clearing, but this won't work with the Gotoh P1 and Q1
	  matrices.

2002-11-25 02:51  twu

	* stage3.c, src/stage3.c, pair.c, src/pair.c: Changed definition of
	  coverage to be based on length of query sequence that aligns.

2002-11-25 02:51  twu

	* stage2.c, src/stage2.c: Added a seenone check to protect against
	  long stretches of N's in the genome.

2002-11-25 02:51  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h: Created a
	  Stage1_T object that can hold state, for resuming stage 1
	  calculations later.  Stage1_T contains a list of Matchpair_T
	  objects, and some procedures have been moved to matchpair.c.

2002-11-25 02:49  twu

	* matchpair.c, matchpair.h, src/matchpair.c, src/matchpair.h: Added
	  an object Matchpair_T to hold pairs of Match_T objects.

2002-11-25 02:49  twu

	* params.c, src/params.c, params.h, src/params.h: Added parameters
	  for crossspecies and changed name of maxextend to maxstutter.

2002-11-20 02:10  twu

	* stage3.c, src/stage3.c, dynprog.c, src/dynprog.c, dynprog.h,
	  src/dynprog.h: When calling dynprog, now passing pointers to
	  subsequence rather than copying subsequences.

2002-11-20 01:45  twu

	* block.c, src/block.c, block.h, src/block.h: Simplified procedure
	  for processing oligos by Block_T object.

2002-11-20 01:44  twu

	* params.c, src/params.c, params.h, src/params.h: Added parameters
	  for stage1size and maxlookback.

2002-11-20 01:43  twu

	* pair.c, src/pair.c, pair.h, src/pair.h, stage3.c, src/stage3.c,
	  stage3.h, src/stage3.h: Added counts for unknowns and reporting
	  of coverage.

2002-11-20 01:42  twu

	* oligoindex.c, src/oligoindex.c: Increased size of memory blocks
	  from 10 to 50.

2002-11-20 01:39  twu

	* oligoindex.c, src/oligoindex.c: Replaced realloc function with
	  explicit calls to calloc and free, because Third Degree reported
	  occasional errors with realloc.

2002-11-20 01:37  twu

	* mem.c, src/mem.c: Added blank line.

2002-11-20 01:37  twu

	* match.c, src/match.c, match.h, src/match.h: Added procedure for
	  Match_copy and simplified Match_new.

2002-11-20 01:35  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h, indexdb.c,
	  src/indexdb.c, indexdb.h, src/indexdb.h, oligo.c, src/oligo.c,
	  oligo.h, src/oligo.h, snap.c, src/gmap.c, src/snap.c: Major
	  change to stage 1 procedure to work on either 24-mers or 18-mers.

2002-11-20 01:32  twu

	* genome.c, src/genome.c: Inlined procedure fill_buffer.

2002-11-20 00:22  twu

	* genome.c, src/genome.c: Simplified routine for fill_buffer.

2002-11-14 17:33  twu

	* indexdb.c, src/indexdb.c, indexdb.h, src/indexdb.h: Added code
	  for ignoring poly A hits.  Added procedure for reading 12-mer
	  positions.

2002-11-14 17:32  twu

	* pair.c, src/pair.c: Removed debugging statement.

2002-11-14 17:30  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h, block.c,
	  src/block.c, match.c, src/match.c, match.h, src/match.h, oligo.c,
	  src/oligo.c: Parameterized stage1size.

2002-11-11 15:20  twu

	* pair.c, src/pair.c, pair.h, src/pair.h: Distinguished between
	  mismatches and indels.  Fixed cases where gaps need to be merged
	  (e.g., affy.HGU95A.34233_i_at, which created ===...======...===
	  when an 8-mer fell into a gap and was then aligned to either end
	  of the gap by dynamic programming.

2002-11-11 15:18  twu

	* params.c, src/params.c, params.h, src/params.h: Added flag for
	  low stringency.

2002-11-11 15:18  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h: Changed
	  definition of LARGEQUERYGAP to be maxlookback.  Distinguished
	  between mismatches and indels.

2002-11-11 15:17  twu

	* snap.c, src/gmap.c, src/snap.c: Changed definition of
	  LARGEQUERYGAP to be maxlookback.  Added flag for lowstringency
	  (12-mers).

2002-11-11 15:15  twu

	* stage2.c, src/stage2.c, dynprog.c, src/dynprog.c, dynprog.h,
	  src/dynprog.h: Changed definition of LARGEQUERYGAP to be
	  maxlookback.

2002-11-11 15:15  twu

	* result.c, src/result.c: Improved check on whether to free array
	  in result.

2002-11-11 03:12  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h, params.c,
	  src/params.c, params.h, src/params.h: Made maxlookback a
	  parameter.

2002-11-11 03:12  twu

	* snap.c, src/gmap.c, src/snap.c: Introduced heap memory for each
	  thread for dynamic programming.  Made maxlookback a parameter.

2002-11-11 03:12  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h: Introduced heap
	  memory for each thread for dynamic programming.  Restricted
	  peelback for consecutive positions.

2002-11-11 03:11  twu

	* dynprog.c, src/dynprog.c, dynprog.h, src/dynprog.h: Introduced
	  heap memory for each thread for dynamic programming.

2002-11-08 08:54  twu

	* dynprog.c, src/dynprog.c: Changed dynamic programming procedure
	  to be banded.

2002-11-08 08:53  twu

	* stage2.c, src/stage2.c, stage3.c, src/stage3.c: Revised stage 2
	  procedure to jump every INDEXSIZE, keep track of consecutive
	  matches, and have a maximum lookback.  Changed stage 3 procedure
	  accordingly, including increasing peelback to INDEXSIZE.

2002-11-08 08:13  twu

	* snap.c, src/gmap.c, src/snap.c: Changed default behavior to be
	  ordered output.

2002-11-08 08:12  twu

	* genome.c, src/genome.c: Revmoed pre-loading for genome, and used
	  madvise(MADV_DONTNEED) instead.

2002-11-07 07:33  twu

	* dynprog.c, src/dynprog.c: Added a zero gap penalty on the ends.
	  Changed mismatch penalty to be less than a match penalty, and
	  reduced intron reward accordingly.

2002-11-07 07:29  twu

	* stage3.c, src/stage3.c: Added a peelback on the 5' end, because
	  it's just like half of a paired gap alignment.

2002-11-07 04:26  twu

	* snap.c, src/gmap.c, src/snap.c: Removed hack used for debugging.

2002-11-07 04:26  twu

	* stage2.c, src/stage2.c: Introduced concept of a maximum lookback,
	  and will now go beyond the previous limit if no hit has been
	  found.

2002-11-07 04:25  twu

	* genome.c, src/genome.c: Changed genome to be pre-paged when user
	  specifies it.

2002-11-07 04:25  twu

	* indexdb.c, src/indexdb.c: Changed type of i from int to size_t.

2002-11-06 07:12  twu

	* pair.c, src/pair.c, pair.h, src/pair.h, stage3.c, src/stage3.c:
	  Changed pairs in stage 3 object to be allocated as a separate
	  block, so they can be output at a later time.

2002-11-06 07:10  twu

	* blackboard.c, src/blackboard.c, blackboard.h, src/blackboard.h,
	  reqpost.c, src/reqpost.c, reqpost.h, src/reqpost.h, request.c,
	  src/request.c, request.h, src/request.h, result.c, src/result.c,
	  result.h, src/result.h, snap.c, src/gmap.c, src/snap.c: Updated
	  multithreading system to handle ordered output with better
	  throughput by adding an output queue.

2002-11-06 04:37  twu

	* genome.c, indexdb.c, pair.c, src/genome.c, src/indexdb.c,
	  src/pair.c: Added header for string.h to eliminate compiler
	  warnings about strlen type.

2002-11-06 03:36  twu

	* pairpool.c, src/pairpool.c: Increased chunk size from 10000 to
	  20000.

2002-11-06 03:36  twu

	* stage2.c, src/stage2.c: Added debugging comments to generate a
	  graph.

2002-11-06 03:35  twu

	* stage3.c, src/stage3.c: In-lined calls to List_T and Pair_T
	  accessor functions.

2002-11-06 03:30  twu

	* pair.c, src/pair.c, stage1.c, src/stage1.c: In-lined calls to
	  List_T accessor functions.

2002-11-06 03:28  twu

	* list.c, src/list.c, list.h, src/list.h: Added function to return
	  value of the last element of a list.

2002-11-05 07:34  twu

	* pairpool.c, src/pairpool.c, pairpool.h, src/pairpool.h: Removed
	  calls to realloc(), because they do not preserve pointer values.
	  Replaced with allocation of chunks of memory as needed.

2002-11-05 07:33  twu

	* stage2.c, src/stage2.c, dynprog.c, src/dynprog.c: Changed
	  two-dimensional matrices to be one-dimensional with pointer.

2002-11-05 07:32  twu

	* snap.c, src/gmap.c, src/snap.c: Made minor tweaks to blackboard
	  object, primarily alterating ninputs and noutputs outside the
	  lock, and changing signal of end of output to be a null result.

2002-11-05 07:32  twu

	* reqpost.c, src/reqpost.c, reqpost.h, src/reqpost.h: Added
	  orderedp flag to send only appropriate signals.

2002-11-05 07:29  twu

	* blackboard.h, src/blackboard.h: Made minor tweaks to blackboard
	  object, primarily alterating ninputs and noutputs outside the
	  lock, and changing signal of end of output to be a null result.

2002-11-05 07:29  twu

	* blackboard.c, src/blackboard.c: Made minor tweaks to blackboard
	  object, primarily alterating ninputs and noutputs outside the
	  lock.

2002-11-04 05:12  twu

	* dynprog.c, list.c, listdef.h, pairpool.c, pairpool.h, stage2.c,
	  stage3.c, src/dynprog.c, src/list.c, src/listdef.h,
	  src/pairpool.c, src/pairpool.h, src/stage2.c, src/stage3.c: Added
	  a pool of List_T cells for each thread to reduce heap contention.

2002-11-04 02:46  twu

	* Makefile, blackboard.c, src/blackboard.c, dynprog.c, dynprog.h,
	  genome.c, genome.h, pair.c, pairdef.h, pairpool.c, pairpool.h,
	  reqpost.c, reqpost.h, request.c, request.h, sequence.c,
	  sequence.h, snap.c, stage2.c, stage2.h, stage3.c, stage3.h,
	  src/dynprog.c, src/dynprog.h, src/genome.c, src/genome.h,
	  src/gmap.c, src/pair.c, src/pairdef.h, src/pairpool.c,
	  src/pairpool.h, src/reqpost.c, src/reqpost.h, src/request.c,
	  src/request.h, src/sequence.c, src/sequence.h, src/snap.c,
	  src/stage2.c, src/stage2.h, src/stage3.c, src/stage3.h: Provided
	  each worker thread with separate sources of heap memory for
	  genomic sequence and for Pair_T objects.  Intended to reduce heap
	  contention.

2002-11-04 01:13  twu

	* stage2.c, src/stage2.c: Created define for MAXLOOKBACK.

2002-11-04 01:12  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h: Changed constants
	  to be based on those in indexdb.h.

2002-11-04 01:12  twu

	* indexdb.c, src/indexdb.c, indexdb.h, src/indexdb.h: Changed stage
	  1 lookup to be based on 12-mers, rather than 8-mers.

2002-11-02 15:42  twu

	* indexdb.c, src/indexdb.c: Implemented binary search on third
	  8-mer.

2002-11-02 10:31  twu

	* snap.c, src/gmap.c, src/snap.c: Allowed user to specify full path
	  of database in the -d flag.

2002-11-02 10:30  twu

	* Makefile: Added stopwatch to Makefile.

2002-11-02 10:29  twu

	* indexdb.c, src/indexdb.c: Changed preloading of indexdb to touch
	  each page effectively, not by using memcpy(), which fails to load
	  in pages.

2002-11-02 10:28  twu

	* sequence.c, src/sequence.c: Added check for first call to
	  fgetc(input) being EOF.

2002-11-01 05:54  twu

	* pair.c, src/pair.c: Changed print routine to work properly on
	  user-supplied genomic segments.

2002-11-01 05:53  twu

	* genome.c, src/genome.c, indexdb.c, src/indexdb.c: Changed
	  pre-load to use fread/fopen/fwrite, rather than memcpy, which
	  fails to load the pages into memory.

2002-11-01 05:53  twu

	* Makefile: Changed stage 1 database to use index table of 8-mers,
	  rather than a hash table of 24-mers.

2002-11-01 05:50  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c, block.c, block.h,
	  oligo.c, oligo.h, params.c, params.h, snap.c, stage1.c, stage1.h,
	  src/block.c, src/block.h, src/gmap.c, src/oligo.c, src/oligo.h,
	  src/params.c, src/params.h, src/snap.c, src/stage1.c,
	  src/stage1.h: Changed stage 1 database to use index table of
	  8-mers, rather than a hash table of 24-mers.

2002-11-01 05:48  twu

	* stopwatch.c, stopwatch.h, src/stopwatch.c, src/stopwatch.h: Added
	  stopwatch function to program.

2002-11-01 02:39  twu

	* genome.h, src/genome.h, genome.c, src/genome.c: Added batch mode
	  by using mmap/memcpy, but this appears to fail on a clustered
	  file system.

2002-11-01 02:39  twu

	* indexdb.c, indexdb.h, src/indexdb.c, src/indexdb.h: Implemented
	  Indexdb_T as a substitute for Hashdb_T.

2002-10-31 02:05  twu

	* stage2.c, src/stage2.c: Changed stage 2 procedure to consider
	  both forward and reverse complement introns in one pass.  Fixed a
	  small bug in intron_score to require position >= 2.

2002-10-29 04:31  twu

	* stage2.c, stage3.c, src/stage2.c, src/stage3.c: Replaced calls to
	  Sequence_char with direct array access.

2002-10-29 04:14  twu

	* Makefile, blackboard.h, genome.c, genome.h, hashdb-read.c,
	  match.c, offset.c, oligoindex.c, pair.c, reqpost.c, reqpost.h,
	  segmentpos.c, src/blackboard.h, src/genome.c, src/genome.h,
	  src/match.c, src/oligoindex.c, src/pair.c, src/reqpost.c,
	  src/reqpost.h, src/segmentpos.c, snap.c, stage2.c, stage3.c,
	  src/gmap.c, src/snap.c, src/stage2.c, src/stage3.c: Made various
	  fixes for compiler warnings.

2002-10-29 03:43  twu

	* stage3.c, src/stage3.c: Separated procedures for middle single
	  gap and end single gap.  Decreased size of single gap dynamic
	  programming procedure for 5' and 3' ends to have genomejump =
	  2*queryjump.

2002-10-29 03:42  twu

	* snap.c, src/gmap.c, src/snap.c: Increased default extension to
	  30000 nt.

2002-10-29 03:41  twu

	* dynprog.c, src/dynprog.c: Prevented horizontal jumps on 3' end of
	  splice site.	Adjusted score parameters.

2002-10-28 09:35  twu

	* dynprog.c, oligoindex.h, stage2.c, src/dynprog.c,
	  src/oligoindex.h, src/stage2.c: Changed oligomer size in stage 2
	  from 10 to 8, and adjusted dynamic programming parameters
	  accordingly.	Prevented genomic gap at the 5' edge of an intron.
	  Made initial cdna_direction test more robust.

2002-10-28 09:33  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed calls to SNAP that don't
	  involve any sequence (the -C and -L flags).

2002-10-28 09:32  twu

	* stage3.c, src/stage3.c: Reduced minimum intron size from 10 to 9.

2002-10-28 09:31  twu

	* stage1.c, src/stage1.c: Substituted the constant HASHSIZE for 24.

2002-10-28 00:06  twu

	* dynprog.c, src/dynprog.c: Increased reward for intron.  A score
	  of 10 fails to identify a canonical intron with a gap.

2002-10-28 00:05  twu

	* pair.c, src/pair.c: Fixed misreporting of query start coordinate.

2002-10-28 00:05  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed small memory leak.

2002-10-27 14:48  twu

	* Makefile, dynprog.c, splice-site.c, splice-site.h, src/dynprog.c:
	  Added splice site calculations to find best intron.

2002-10-27 13:17  twu

	* dynprog.c, src/dynprog.c, dynprog.h, stage2.c, stage2.h,
	  stage3.c, stage3.h, src/dynprog.h, src/stage2.c, src/stage2.h,
	  src/stage3.c, src/stage3.h: Improved stage 2 dynamic programming
	  procedure to consider introns (only for consecutive query
	  positions), to compute gap penalty based on difference of
	  genomejump and queryjump, and to consider cDNA directions
	  separately.

2002-10-27 13:15  twu

	* snap.c, src/gmap.c, src/snap.c: Improved handling of arguments
	  for database search and for alignment to genomic segment.

2002-10-27 13:13  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h: Fixed stage 1 to
	  consider Watson and Crick strands separately.

2002-10-27 08:26  twu

	* params.c, src/params.c, params.h, src/params.h, stage1.c,
	  src/stage1.c, stage1.h, src/stage1.h, snap.c, src/gmap.c,
	  src/snap.c: Made extension in stage 1 a user-definable parameter.

2002-10-27 01:36  twu

	* blackboard.c, blackboard.h, pair.c, request.c, request.h,
	  sequence.c, sequence.h, snap.c, src/blackboard.c,
	  src/blackboard.h, src/gmap.c, src/pair.c, src/request.c,
	  src/request.h, src/sequence.c, src/sequence.h, src/snap.c:
	  Provided ability to align cDNA against user-provided genomic
	  segment.

2002-10-27 01:34  twu

	* dynprog.c, src/dynprog.c: Gave credit to half introns.

2002-10-25 17:40  twu

	* genome.c, genome.h, oligoindex.c, oligoindex.h, snap.c, stage1.c,
	  stage1.h, stage2.c, stage2.h, stage3.c, stage3.h, src/genome.c,
	  src/genome.h, src/gmap.c, src/oligoindex.c, src/oligoindex.h,
	  src/snap.c, src/stage1.c, src/stage1.h, src/stage2.c,
	  src/stage2.h, src/stage3.c, src/stage3.h: Changed genomicseg to
	  be of type Sequence_T.

2002-10-25 17:39  twu

	* block.c, src/block.c: Changed debug flag.

2002-10-25 16:16  twu

	* Makefile, request.c, request.h, sequence.c, sequence.h, snap.c,
	  stage1.c, stage1.h, stage2.c, stage2.h, src/gmap.c,
	  src/request.c, src/request.h, src/sequence.c, src/sequence.h,
	  src/snap.c, src/stage1.c, src/stage1.h, src/stage2.c,
	  src/stage2.h, stage3.c, stage3.h, src/stage3.c, src/stage3.h:
	  Renamed Queryseq_T to Sequence_T.

2002-10-25 15:58  twu

	* queryseq.c, queryseq.h: Renamed Queryseq_T to Sequence_T, to
	  allow genomic sequences to be represented this way.

2002-10-25 15:55  twu

	* result.c, src/result.c, result.h, src/result.h, params.c,
	  src/params.c, params.h, src/params.h: Allowed first-order
	  approximation using stage1 results.

2002-10-25 15:54  twu

	* stage3.c, src/stage3.c, stage3.h, src/stage3.h, pair.c,
	  src/pair.c, pair.h, src/pair.h: Simplified argument lists of some
	  functions.

2002-10-25 15:54  twu

	* stage2.c, src/stage2.c: Increased extension on left and right to
	  find small terminal exons.

2002-10-25 15:53  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h: Fixed assessment
	  of whether getpair succeeded or failed.

2002-10-25 15:52  twu

	* match.c, src/match.c, match.h, src/match.h, snap.c, src/gmap.c,
	  src/snap.c: Added first-order approximation, to use just stage1
	  results.

2002-10-25 15:51  twu

	* block.c, src/block.c, block.h, src/block.h, oligo.c, src/oligo.c:
	  Fixed bugs in Block_next_to_stoppos when the query sequence has
	  many non-ACGT characters.

2002-10-25 04:14  twu

	* snap.c, src/gmap.c, src/snap.c, Makefile: Made compressed genome
	  the default.

2002-10-25 04:14  twu

	* hashdb-write.c, hashdb-read.c: Reverted to old hashtable format,
	  which contains only two arrays.

2002-10-24 09:21  twu

	* dynprog.c, src/dynprog.c, dynprog.h, src/dynprog.h, pair.c,
	  src/pair.c, pair.h, src/pair.h, params.c, src/params.c, params.h,
	  src/params.h, stage3.c, src/stage3.c, stage3.h, src/stage3.h,
	  snap.c, src/gmap.c, src/snap.c: Added diagnostic mode to print
	  out asterisks instead of vertical bars where dynamic programming
	  was done.

2002-10-24 09:20  twu

	* genome.c, src/genome.c, genome.h, src/genome.h: Added ability to
	  read compressed genomes.

2002-10-24 06:11  twu

	* Makefile, gencompress.c: Added compression routine for genomes.

2002-10-24 06:10  twu

	* blackboard.c, src/blackboard.c, blackboard.h, src/blackboard.h,
	  reqpost.c, src/reqpost.c, reqpost.h, src/reqpost.h, snap.c,
	  src/gmap.c, src/snap.c: Added anyorder behavior to blackboard,
	  and made it default.

2002-10-22 13:34  twu

	* stage2.c, src/stage2.c: Removed code for memory freeing of
	  positions, which is now performed by Oligoindex_T.

2002-10-22 13:33  twu

	* oligoindex.c, src/oligoindex.c: Changed type of positions from
	  void ** to unsigned int **, to make code clearer and more robust.

2002-10-22 08:00  twu

	* pair.c, src/pair.c, pair.h, src/pair.h, params.c, src/params.c,
	  params.h, src/params.h, snap.c, src/gmap.c, src/snap.c, stage3.c,
	  src/stage3.c, stage3.h, src/stage3.h: Added option to print
	  universal genomic coordinates.

2002-10-22 07:56  twu

	* genome.c, src/genome.c, hashdb-read.c: Changed mmap to from
	  MAP_PRIVATE to MAP_SHARED.

2002-10-22 05:12  twu

	* genome.c, src/genome.c, genome.h, src/genome.h, params.c,
	  src/params.c, params.h, src/params.h, snap.c, src/gmap.c,
	  src/snap.c, stage2.c, src/stage2.c, stage2.h, src/stage2.h:
	  Changed Genome_T to be memory-mapped, rather than using fopen,
	  which is needed for multithreading.

2002-10-22 04:51  twu

	* stage1.c, src/stage1.c: Fixed bug where salvage procedure fails
	  to find anything.

2002-10-22 04:50  twu

	* mem.c, src/mem.c: Enhanced mem.c to give actual location of
	  failure.

2002-10-22 04:30  twu

	* oligoindex.c, src/oligoindex.c, oligoindex.h, src/oligoindex.h,
	  stage2.c, src/stage2.c, stage2.h, src/stage2.h, snap.c,
	  src/gmap.c, src/snap.c: Changed algorithm for stage 2 to allocate
	  genomic positions dynamically in Oligoindex_T.  To limit number
	  of positions stored, we prescan the queryseq to see what
	  oligomers are relevant.

2002-10-22 01:41  twu

	* stage2.c, src/stage2.c: Reverted back to previous Stage 2
	  strategy where we stored genomic sequence in oligoindex and
	  scanned query sequence.

2002-10-22 01:40  twu

	* oligoindex.c, src/oligoindex.c, oligoindex.h, src/oligoindex.h:
	  Simplified routines greatly.

2002-10-21 16:57  twu

	* stage2.c, src/stage2.c: Changed stage 2 strategy to index the
	  query sequence rather than the genomic sequence.  This should
	  result in some speed up.

2002-10-21 16:56  twu

	* reader.c, reader.h, src/reader.c, src/reader.h, stage1.c,
	  src/stage1.c: Made Reader_new function depend on sequence rather
	  than Queryseq_T object.

2002-10-21 16:55  twu

	* list.c, src/list.c, list.h, src/list.h: Added function
	  List_index.

2002-10-21 16:55  twu

	* oligoindex.c, oligoindex.h, src/oligoindex.c, src/oligoindex.h:
	  Hard-coded interval, rather than passing it in.

2002-10-21 15:42  twu

	* snap.c, src/gmap.c, src/snap.c, pair.c, src/pair.c: Added flag to
	  avoid showing contig coordinates.

2002-10-21 10:43  twu

	* params.c, params.h, src/params.c, src/params.h: Added Params_T
	  object.

2002-10-21 10:42  twu

	* Makefile, blackboard.c, blackboard.h, reqpost.c, reqpost.h,
	  src/blackboard.c, src/blackboard.h, src/reqpost.c, src/reqpost.h,
	  request.c, request.h, result.c, result.h, snap.c, src/gmap.c,
	  src/request.c, src/request.h, src/result.c, src/result.h,
	  src/snap.c: Major change to make program multithreaded.
	  Introduced Blackboard_T, new Reqpost_T, and new Result_T objects.

2002-10-21 10:41  twu

	* stage3.h, src/stage3.h: Added header file.

2002-10-21 10:41  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h: Cleaned up
	  procedures.  Passed in querylength via queryseq.

2002-10-21 10:40  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h: Cleaned up
	  procedures.  Made hashinterval a constant.

2002-10-21 10:40  twu

	* queryseq.c, sequence.c, src/sequence.c: Removed macro for DEBUG2.

2002-10-21 10:38  twu

	* oligoindex.c, src/oligoindex.c, oligoindex.h, src/oligoindex.h:
	  Allowed offsets for oligoindex to be created separately (for
	  individual worker threads.)

2002-10-21 10:37  twu

	* block.c, src/block.c: Changed name from Result_T to Match_T.

2002-10-21 05:37  twu

	* block.c, match.c, match.h, stage1.c, stage1.h, stage2.c,
	  stage2.h, src/block.c, src/match.c, src/match.h, src/stage1.c,
	  src/stage1.h, src/stage2.c, src/stage2.h: Changed name of
	  Result_T to Match_T.

2002-10-21 05:08  twu

	* result.c, result.h, src/result.c, src/result.h: Renamed Result_T
	  to Match_T.

2002-10-21 04:37  twu

	* stage3.c, src/stage3.c: Turned off debug statements.

2002-10-20 11:29  twu

	* queryseq.c, sequence.c, src/sequence.c: Fixed small memory leak.

2002-10-20 11:27  twu

	* stage3.c, stage3.h, src/stage3.c, src/stage3.h, align.c,
	  stage2.c, stage2.h, src/stage2.c, src/stage2.h, align.h, snap.c,
	  src/gmap.c, src/snap.c, Makefile: Created Stage 3 and moved part
	  of Stage 2 commands there.

2002-10-20 07:12  twu

	* Makefile, align.c, align.h, queryseq.c, queryseq.h, reader.c,
	  reader.h, sequence.c, sequence.h, snap.c, stage1.c, stage1.h,
	  stage2.c, stage2.h, src/gmap.c, src/reader.c, src/reader.h,
	  src/sequence.c, src/sequence.h, src/snap.c, src/stage1.c,
	  src/stage1.h, src/stage2.c, src/stage2.h: Added a separate
	  Queryseq_T object, and moved some functions from Reader to
	  Querypos.

2002-10-20 07:08  twu

	* pair.c, src/pair.c: Removed bottom ruler.

2002-10-20 04:34  twu

	* block.c, block.h, snap.c, stage1.c, src/block.c, src/block.h,
	  src/gmap.c, src/snap.c, src/stage1.c, stage1.h, src/stage1.h:
	  Removed multithreading from stage 1 (hash table reads).

2002-10-20 04:33  twu

	* dynprog.c, src/dynprog.c: Made maximize_entry inline to speed up
	  dynamic programming.

2002-10-20 04:32  twu

	* stage2.c, src/stage2.c: Added another 24 (hashsize) to
	  extensions.  Without this, for some reason, we miss the ends.

2002-10-20 02:31  twu

	* dynprog.c, src/dynprog.c, penalties.c, penalties.h, Makefile:
	  Removed Penalties_T object in order to increase speed.

2002-10-20 02:30  twu

	* stage2.c, src/stage2.c: Changed extension to be based on
	  remaining distance from end.

2002-10-19 15:24  twu

	* snap.c, src/gmap.c, src/snap.c: Eliminated parameters maxentries
	  and indexsize.

2002-10-19 15:23  twu

	* oligoindex.c, src/oligoindex.c, oligoindex.h, src/oligoindex.h:
	  Made changes to improve speed, by eliminating unnecessary arrays.

2002-10-19 15:23  twu

	* stage2.c, src/stage2.c, stage2.h, src/stage2.h: Made changes to
	  improve speed, including making build_pairs_middle iterative and
	  using the fill_oligo function where possible.

2002-10-19 15:21  twu

	* align.c: Changed Pair_T object to reflect the actual case of the
	  query sequence.

2002-10-19 07:08  twu

	* oligoindex.c, src/oligoindex.c: Simplified construction of
	  Oligoindex_T object.

2002-10-19 02:06  twu

	* Makefile, align.c, align.h, oligoindex.c, oligoindex.h, snap.c,
	  stage2.c, stage2.h, src/gmap.c, src/oligoindex.c,
	  src/oligoindex.h, src/snap.c, src/stage2.c, src/stage2.h: Made
	  indexsize a hardcoded parameter.  Allocated space for Oligoindex
	  once at beginning of program.

2002-10-19 00:42  twu

	* align.c, stage2.c, src/stage2.c: Using Pair_T object instead of
	  Result_T object throughout stage 2.

2002-10-19 00:41  twu

	* stage1.c, src/stage1.c: Fixed memory leak.

2002-10-18 19:54  twu

	* stage2.c, src/stage2.c, align.c, align.h: Major change to improve
	  stage 2 efficiency.  Using arrays instead of lists for the
	  dynamic programming alignment.

2002-10-18 19:52  twu

	* oligoindex.c, src/oligoindex.c: Changed debug statements from
	  fprintf to printf.

2002-10-18 18:30  twu

	* offset.h, offset.c: Added back to repository.

2002-10-18 09:09  twu

	* stage1.c, src/stage1.c, stage2.c, src/stage2.c: Allowed
	  alignments even if we can't find a matching pair on the 5' and 3'
	  ends.

2002-10-18 09:07  twu

	* oligoindex.c, src/oligoindex.c: Changed debug statements.

2002-10-18 09:07  twu

	* align.c: Removed debug statement.

2002-10-18 01:42  twu

	* Makefile: Added rule for counting lines of code.

2002-10-17 05:15  twu

	* match.c, result.c, src/match.c, src/result.c, match.h, result.h,
	  src/match.h, src/result.h: Cleaned up unused or obsolete
	  procedures.

2002-10-17 05:14  twu

	* Makefile, snap.c, src/gmap.c, src/snap.c, snapgenerate.c:
	  Generated dump procedure to work on either the text offset file
	  or the offset BerkeleyDB.  Added accession length to the output.

2002-10-17 05:13  twu

	* hashdb-read.c: Made hashindex memory mapped again.  Added
	  madvise() commands to help with memory mapping.

2002-10-17 05:10  twu

	* segmentpos.c, src/segmentpos.c, segmentpos.h, src/segmentpos.h:
	  Generated dump procedure to work on either the text offset file
	  or the offset BerkeleyDB.  Added accession length to the output.

2002-10-17 05:10  twu

	* stage1.c, src/stage1.c: Changed algorithm for stage 1 to extend
	  for 2 hash intervals past the first connectable pair of hits.

2002-10-17 05:08  twu

	* block.c, src/block.c, block.h, src/block.h: Added ability to stop
	  block at a certain position.

2002-10-15 06:07  twu

	* dynprog.c, dynprog.h, stage1.c, stage2.c, src/dynprog.c,
	  src/dynprog.h, src/stage1.c, src/stage2.c: Added counts of
	  matches and mismatches on dynamic programming of single gaps, and
	  used this to exclude dynamic programming results on 5' and 3'
	  ends.

2002-10-15 05:34  twu

	* snap.c, stage2.c, stage2.h, src/gmap.c, src/snap.c, src/stage2.c,
	  src/stage2.h: Increased EXTENSION from 90 to 1000.  Included
	  check for genomicpos2 against chromosomal length.

2002-10-15 05:33  twu

	* hashdb-read.c, hashdb-write.c: Reading hashindex into memory
	  instead of memory mapping it.

2002-10-15 01:09  twu

	* dynprog.c, src/dynprog.c: Cosmetic changes to debug macro.

2002-10-15 01:05  twu

	* align.c: Cleaned out unused code.

2002-10-15 01:05  twu

	* snap.c, src/gmap.c, src/snap.c: Added flag for specifying
	  maxentries (in stage 2).

2002-10-15 01:04  twu

	* stage2.c, src/stage2.c: Fixed one-off error on requesting dynamic
	  programming of 5' end.

2002-10-14 16:34  twu

	* hashdb-write.h: Added log file.

2002-10-14 16:33  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Fixed minor bug
	  relating to log file.

2002-10-14 16:24  twu

	* hashdb-write.c: Added file pointer for a log file.

2002-10-14 16:24  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Raised default
	  maxentries value from 5 to 20.  Added file pointer for a log
	  file.

2002-10-14 14:22  twu

	* hashdb-write.c: Commented out monitoring statements.

2002-10-14 14:21  twu

	* hashdb.c: Developed new hash function to give the same hash value
	  for an oligo and its reverse complement.  This should improve
	  page access for the hash lookup.

2002-10-14 14:20  twu

	* stage2.c, src/stage2.c: Improved debugging statement.

2002-10-14 14:20  twu

	* snap.c, src/gmap.c, src/snap.c: Removed effect of maxentries in
	  stage 2, which was causing some alignments to be short.

2002-10-14 14:17  twu

	* align.c: Changed debug statements from fprintf to printf.

2002-10-14 09:28  twu

	* hashdb-read.c: Fixed problem in binary search where we subtracted
	  1U from 0U.

2002-10-14 09:27  twu

	* dynprog.c, src/dynprog.c: Allowed dynamic programming to identify
	  introns even if lowercase.

2002-10-13 18:10  twu

	* database.c: Reformatting.

2002-10-13 18:10  twu

	* hashdb-read.c: Fixed bug where function was returning NULL
	  prematurely.

2002-10-13 18:10  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Made second pass
	  read only on auxfile.

2002-10-13 14:13  twu

	* Makefile, block.h, database.c, src/block.h, database.h, match.c,
	  oligo.h, request.h, result.c, snap.c, snapindex.c, stage1.h,
	  src/gmap.c, src/gmapindex.c, src/match.c, src/oligo.h,
	  src/request.h, src/result.c, src/snap.c, src/snapindex.c,
	  src/stage1.h: Removed traces of PureDB package.

2002-10-13 14:05  twu

	* Makefile, cell.c, cell.h, snapindex.c, src/gmapindex.c,
	  src/snapindex.c: Changed snapindex program to a two-pass process.
	  The first pass saves the .aux file, and the second pass creates
	  the hash table.  This simplifies the Cell_T object greatly.

2002-10-13 04:17  twu

	* cell.c, cell.h, hashdb-write.c, snapindex.c, src/gmapindex.c,
	  src/snapindex.c: Sorting cell entries by hashvalue then by oligo.

2002-10-12 12:13  twu

	* hashdb-read.c: Fixed minor bug in binary search routine.

2002-10-11 09:28  twu

	* Makefile, block.c, hashdb-read.c, hashdb-write.c, src/block.c:
	  Changed structure of hashdb to have three tables: oligo_offset,
	  oligos, and positions.

2002-10-11 03:20  twu

	* hashdb-write.c: Checking totalsize of contents and setting file
	  size initially to that.

2002-10-11 03:19  twu

	* hashdb-read.c: Memory mapping hash contents now.

2002-10-10 12:32  twu

	* snapgenerate.c: Fixed memory leaks.

2002-10-10 12:27  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed memory leak from failure to
	  free Offset_T object.

2002-10-10 12:25  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed bug where datadir was
	  freed.

2002-10-10 12:25  twu

	* hashdb-read.c: Fixed bug where memory mapped offsets were freed.

2002-10-10 12:24  twu

	* dynprog.c, src/dynprog.c: Fixed bug where cL+1 or cL+2 exceeded
	  length2L.

2002-10-10 11:10  twu

	* oligo.c, src/oligo.c: Revised procedures to handle lowercase
	  letters in the query sequence.

2002-10-10 11:09  twu

	* hashdb-read.c: Fixed bug where nentries wasn't being set.

2002-10-10 10:59  twu

	* Makefile: Divided hashdb into separate read and write files.

2002-10-10 10:59  twu

	* snap.c, src/gmap.c, src/snap.c: Changing from PureDB to our own
	  Hashdb_T.

2002-10-10 10:58  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h: Changing from
	  PureDB to our own Hashdb_T.  Also fixed bug where results3 was
	  not being initialized to NULL.

2002-10-10 10:58  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Divided hashdb
	  file into a separate read and write file.

2002-10-10 10:57  twu

	* snapgenerate.c: Using Offset_T object now, after we have written
	  the chromosome file.

2002-10-10 10:56  twu

	* hashdb-write.c: Fixed bug causing unaligned access errors, by
	  splitting header into two 4-byte unsigned ints.

2002-10-10 10:56  twu

	* hashdb-read.c: Fixed bug where length = 0.  Also fixed bug
	  causing unaligned access errors, by splitting header into two
	  4-byte unsigned ints.

2002-10-10 10:54  twu

	* block.c, src/block.c, block.h, src/block.h, oligo.c, src/oligo.c,
	  oligo.h, src/oligo.h, request.c, src/request.c, request.h,
	  src/request.h: Changing from PureDB to our own Hashdb_T.

2002-10-10 08:28  twu

	* hashdb-read.c, hashdb-read.h, hashdb-write.c, hashdb-write.h,
	  hashdb.c, hashdb.h: Split Hashdb functions into separate read and
	  write files.

2002-10-10 07:31  twu

	* hashdb.c, hashdb.h: Provided option to switch between unsigned
	  long and unsigned int for hashoffset_t.

2002-10-10 06:12  twu

	* hashdb.c, hashdb.h: Changed offsets to be memory-mapped rather
	  than read by file.

2002-10-10 06:03  twu

	* Makefile, hashdb.c, hashdb.h, snapindex.c, src/gmapindex.c,
	  src/snapindex.c: Changing hash database to our own format.

2002-10-10 01:56  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Fixed bug where
	  last oligo would not get stored.

2002-10-09 10:15  twu

	* pair.c, segmentpos.c, src/pair.c, src/segmentpos.c: Added missing
	  header file for commafmt.

2002-10-09 10:15  twu

	* Makefile: Revised object files needed for snapindex and
	  snapgenerate.

2002-10-09 10:10  twu

	* Makefile, accpos.c, add-chrpos-to-endpoints.c, block.c, block.h,
	  cell.c, database.c, database.h, match.c, match.h, offsetdb.c,
	  offsetdb.h, result.c, result.h, segmentpos.c, segmentpos.h,
	  snap.c, snapgenerate.c, snapindex.c, stage1.c, stage1.h,
	  src/block.c, src/block.h, src/gmap.c, src/gmapindex.c,
	  src/match.c, src/match.h, src/result.c, src/result.h,
	  src/segmentpos.c, src/segmentpos.h, src/snap.c, src/snapindex.c,
	  src/stage1.c, src/stage1.h: Changed offset reads from a database
	  to a structure read from a flat file.

2002-10-09 10:09  twu

	* get-genome.c, src/get-genome.c: Added -U flag to generate
	  unmasked sequences.

2002-10-09 05:25  twu

	* offset.c, offset.h: Renamed files from offset.* to offsetdb.h

2002-10-09 04:50  twu

	* snap.c, src/gmap.c, src/snap.c: Implemented print_details.

2002-10-09 04:49  twu

	* stage1.c, src/stage1.c, stage1.h, src/stage1.h: Implemented
	  print_details.  Fixed problem where dominated bounds were not
	  being eliminated.

2002-10-09 04:39  twu

	* stage2.c, src/stage2.c: Increased the peelback to identify
	  introns.  Added debugging statements.

2002-10-09 04:38  twu

	* align.c: Fixed greediness for finding introns.  Removed gap
	  penalty and reward for intron.  Instead, implemented a tie
	  breaker for scores based on genomic distance.  Increased the
	  peelback to identify introns.

2002-10-08 10:34  twu

	* align.c, block.c, match.c, match.h, result.c, result.h, snap.c,
	  stage1.c, stage1.h, stage2.c, src/block.c, src/gmap.c,
	  src/match.c, src/match.h, src/result.c, src/result.h, src/snap.c,
	  src/stage1.c, src/stage1.h, src/stage2.c: Changed stage 1 of
	  algorithm to find bounds using 5' and 3' hits.

2002-10-07 19:52  twu

	* Makefile, pair.c, pair.h, stage2.c, src/pair.c, src/pair.h,
	  src/stage2.c: Changed goodness to be differences of matches and
	  mismatches.

2002-10-07 09:04  twu

	* dynprog.c, src/dynprog.c: Changed recursive functions of
	  traceback and scoreback to be iterative.

2002-10-07 08:51  twu

	* snap.c, src/gmap.c, src/snap.c, stage2.c, src/stage2.c: Added
	  check for large query gaps and avoided doing dynamic programming
	  on those.  Also added check for allpaths being NULL from stage 2.

2002-10-07 08:47  twu

	* align.c: Toggled DEBUG.

2002-10-07 07:48  twu

	* Makefile, snap.c, stage2.c, stage2.h, src/gmap.c, src/snap.c,
	  src/stage2.c, src/stage2.h: Added ability to print alignment
	  summaries only.

2002-10-07 04:52  twu

	* pair.c, src/pair.c: Ignored N's in computing percent identity.

2002-10-07 04:45  twu

	* Makefile, pair.c, pair.h, stage2.c, src/pair.c, src/pair.h,
	  src/stage2.c: Added number of exons to calculations and output.

2002-10-07 04:25  twu

	* snap.c, stage2.c, stage2.h, src/gmap.c, src/snap.c, src/stage2.c,
	  src/stage2.h: Made alignment procedure the default.  Now sorting
	  paths based on the goodness of the alignment.

2002-10-07 04:08  twu

	* pair.c, pair.h, stage2.c, src/pair.c, src/pair.h, src/stage2.c:
	  Removed npairs from some parameter lists.

2002-10-07 04:00  twu

	* pair.c, pair.h, stage2.c, stage2.h, src/pair.c, src/pair.h,
	  src/stage2.c, src/stage2.h: Added calculation for goodness, based
	  on percent identity.

2002-10-07 03:44  twu

	* match.c, pair.c, pair.h, result.c, segmentpos.c, segmentpos.h,
	  snap.c, stage2.c, stage2.h, src/gmap.c, src/match.c, src/pair.c,
	  src/pair.h, src/result.c, src/segmentpos.c, src/segmentpos.h,
	  src/snap.c, src/stage2.c, src/stage2.h: Now printing endpoints
	  based on alignments, if available.

2002-10-07 02:34  twu

	* list.c, src/list.c: Fixed bug in List_last.

2002-10-07 02:29  twu

	* list.c, list.h, src/list.c, src/list.h: Added a List_last
	  procedure.

2002-10-07 01:36  twu

	* Makefile, match.c, match.h, result.c, result.h, snap.c, stage1.c,
	  stage1.h, stage2.c, stage2.h, src/gmap.c, src/match.c,
	  src/match.h, src/result.c, src/result.h, src/snap.c,
	  src/stage1.c, src/stage1.h, src/stage2.c, src/stage2.h: Created a
	  Stage2_T object and reorganized calculations, in preparation for
	  using the alignments to rank the results.

2002-10-07 00:21  twu

	* Makefile, snap.c, src/gmap.c, src/snap.c: Added parameter for
	  maxaligns, the maximum number of alignments to print.

2002-10-06 16:32  twu

	* dynprog.c, src/dynprog.c: Fixed read of unallocated hash.

2002-10-06 16:32  twu

	* align.c: Fixed read of uninitialized variable.

2002-10-06 15:44  twu

	* align.c, dynprog.c, pair.c, pair.h, stage2.c, src/dynprog.c,
	  src/pair.c, src/pair.h, src/stage2.c: Added ability to recognize
	  introns in revcomp direction, and to print correct indices for
	  Crick strand matches.

2002-10-06 15:23  twu

	* match.c, result.c, src/match.c, src/result.c: Simplified use of
	  zerobasedp.

2002-10-06 15:22  twu

	* snap.c, stage1.c, stage2.c, src/gmap.c, src/snap.c, src/stage1.c,
	  src/stage2.c, stage1.h, stage2.h, src/stage1.h, src/stage2.h:
	  Changed variable names to distinguish between hashsize and
	  indexsize.

2002-10-06 08:22  twu

	* dynprog.c, genome.c, stage2.c, src/dynprog.c, src/genome.c,
	  src/stage2.c: Fixed errors with the sequence and genomic indices.

2002-10-06 06:15  twu

	* stage1.c, src/stage1.c: Removed list reversal to match new scheme
	  for doing stage 1 dynamic programming.

2002-10-06 05:45  twu

	* align.c, pair.c, src/pair.c: Enhanced debugging information.

2002-10-06 05:23  twu

	* align.c: Revised code to make sure that we don't pick unwanted
	  paths after the first.  We set the usedp flags and recompute
	  dynamic programming on subsequent rounds to avoid using those
	  results.  This should affect only stage 1, because maxpaths
	  equals 1 on stage2.

2002-10-06 05:11  twu

	* align.c: Removed gappenalty for stage 1 computation.	This was
	  causing problems with multiple paths for HER2.

2002-10-06 03:08  twu

	* pair.c, src/pair.c, pair.h, stage2.c, src/pair.h, src/stage2.c:
	  Added procedure for summary of exons.

2002-10-06 03:07  twu

	* snap.c, src/gmap.c, src/snap.c: Made printout slightly better.

2002-10-06 03:07  twu

	* match.c, result.c, src/match.c, src/result.c: Fixed miscount on
	  number of matches.

2002-10-06 01:27  twu

	* pair.c, src/pair.c: No change.

2002-10-06 01:27  twu

	* genome.c, src/genome.c, genome.h, src/genome.h: Added modules to
	  retrieve genome sequences.

2002-10-06 01:24  twu

	* dynprog.c, src/dynprog.c: Minor restructuring of procedures.

2002-10-06 01:08  twu

	* dynprog.c, src/dynprog.c: Fixed coordinates in gap.  Changed gap
	  output for non-introns.

2002-10-06 00:58  twu

	* pair.c, src/pair.c: Added printing of rulers in alignments.

2002-10-06 00:45  twu

	* stage2.c, src/stage2.c: Fixed memory leaks.

2002-10-05 16:21  twu

	* dynprog.c, src/dynprog.c: Fixed major problem in paired gap
	  assessments.	Need to subtract, not add, the entry in the right
	  matrix.

2002-10-05 14:56  twu

	* stage2.c, src/stage2.c: Changed criteria for single and paired
	  gaps, based on a minimum intron length.  Created special case for
	  the 3' end.

2002-10-05 14:53  twu

	* penalties.c: Changed middle gap penalties to have bigger opening
	  and smaller extend penalties.

2002-10-05 14:52  twu

	* dynprog.c, src/dynprog.c, dynprog.h, src/dynprog.h: Changed
	  concepts from short and long gaps to single and paired gaps.

2002-10-05 11:48  twu

	* stage2.c, src/stage2.c: Added peelback procedure to help identify
	  correct intron.  Otherwise, the greedy oligo matching procedure
	  can mask the intron boundaries.

2002-10-05 11:47  twu

	* dynprog.c, src/dynprog.c: Fixed bug for traceback on longgap,
	  where we didn't start from the lower right cell.

2002-10-05 11:11  twu

	* align.c, stage2.c, src/stage2.c: Increased size of stage 2 oligos
	  from 8 to 10.

2002-10-05 09:51  twu

	* align.c, oligoindex.c, oligoindex.h, snap.c, stage2.c, stage2.h,
	  src/gmap.c, src/oligoindex.c, src/oligoindex.h, src/snap.c,
	  src/stage2.c, src/stage2.h: Added ability to limit maxentries in
	  stage 2.

2002-10-05 09:51  twu

	* dynprog.c, src/dynprog.c: Changed alignment character for dynamic
	  programming to help with debugging.

2002-10-05 04:01  twu

	* dynprog.c, stage2.c, src/dynprog.c, src/stage2.c: Implemented
	  dynamic programming across long gaps.

2002-10-05 00:51  twu

	* dynprog.c, src/dynprog.c: Reordered priorities in traceback to be
	  (1) continue in same direction, (2) diagonal, (3) vertical, and
	  (4) horizontal.

2002-10-05 00:33  twu

	* dynprog.c, dynprog.h, penalties.c, penalties.h, stage2.c,
	  src/dynprog.c, src/dynprog.h, src/stage2.c: Cleaned up dynamic
	  programming code for the three cases of FIVE, MIDDLE, and THREE.
	  Added stub for dynamic programming of long gaps.

2002-10-04 23:50  twu

	* pair.c, pair.h, src/pair.c, src/pair.h, stage2.c, src/stage2.c:
	  Made improvements to the alignment output.

2002-10-04 10:36  twu

	* pair.c, src/pair.c, match.c, pair.h, result.c, snap.c, stage2.c,
	  src/gmap.c, src/match.c, src/pair.h, src/result.c, src/snap.c,
	  src/stage2.c: Added improvements to the alignment output.

2002-10-04 10:24  twu

	* stage2.c, src/stage2.c: Added code to handle the 5' end properly.

2002-10-04 10:23  twu

	* penalties.c: Changed some values for the penalty parameters.

2002-10-04 10:22  twu

	* dynprog.c, src/dynprog.c: Changed opening penalties to not
	  include the extension.  Added special procedures for 5' and 3'
	  ends of sequence, essentially implementing part of Smith-Waterman
	  on each end.	Added special cases in traceback for 5' and 3'
	  ends, but may not be necessary in light of the other changes.

2002-10-04 07:38  twu

	* stage2.c, src/stage2.c: Added querypos and genomepos to the Pair
	  object.  Reorganized various functions.

2002-10-04 07:37  twu

	* pair.c, src/pair.c, pair.h, src/pair.h: Added querypos and
	  genomepos to the Pair object.

2002-10-04 07:37  twu

	* reader.h, src/reader.h: Added another option to cDNAEnd_T.

2002-10-04 07:37  twu

	* align.c: Fixed the precise bounds around an intron.

2002-10-04 07:33  twu

	* Makefile, dynprog.c, dynprog.h, src/dynprog.c, src/dynprog.h,
	  penalties.c, penalties.h: Added penalties object.  Provided
	  ability to specify different penalties for left, middle, and
	  right part of sequence.

2002-10-04 05:39  twu

	* stage2.c, src/stage2.c: Moved printing procedure to another file.
	  Fixed small bug that caused us to miss printing a base.

2002-10-04 05:39  twu

	* pair.c, pair.h, src/pair.c, src/pair.h: Removed printing of loci
	  names from alignment.

2002-10-04 04:56  twu

	* Makefile, align.c, dynprog.c, dynprog.h, pair.c, stage2.c,
	  src/dynprog.c, src/dynprog.h, src/pair.c, src/stage2.c: Added
	  dynamic programming routine to take care of small gaps.

2002-10-04 00:27  twu

	* Makefile, align.c, align.h, matrix.c, matrix.h, oligoindex.c,
	  oligoindex.h, pair.c, pair.h, path.c, path.h, src/oligoindex.c,
	  src/oligoindex.h, src/pair.c, src/pair.h, match.c, match.h,
	  penalties.c, penalties.h, reader.c, reader.h, result.c, result.h,
	  snap.c, stage1.c, stage1.h, stage2.c, stage2.h, src/gmap.c,
	  src/match.c, src/match.h, src/reader.c, src/reader.h,
	  src/result.c, src/result.h, src/snap.c, src/stage1.c,
	  src/stage1.h, src/stage2.c, src/stage2.h: Major change to
	  algorithm to have two stages: one using hash table (24-mers) and
	  another using an index table (8-mers).  Still need to incorporate
	  a dynamic programming step for gaps in the final alignment.

2002-10-02 08:26  twu

	* whats_on, util/whats_on: Changed program to work with new data
	  directory for alignment results.

2002-10-01 10:55  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed problem where intronlen ==
	  0.  Now requiring intronlen > 0.  Added extra carriage return
	  when zero paths found.

2002-09-27 10:11  twu

	* Makefile: Reduced number of object files used in SNAP.

2002-09-27 10:10  twu

	* get-genome.c, src/get-genome.c: Fixed use of fscanf to match the
	  .chromosome and .contig file format.

2002-09-27 10:09  twu

	* path.c: Simplified call to Path_compute to eliminate scoremat.

2002-09-27 09:45  twu

	* path.h: Simplified call to Path_compute to eliminate scoremat.

2002-09-27 09:44  twu

	* penalties.c, penalties.h: Added procedure to create a default
	  penalties object.

2002-09-27 09:42  twu

	* match.c, result.c, src/match.c, src/result.c: Added line for
	  number of matches.

2002-09-27 09:42  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed bug where resultlist was
	  uninitialized.  Allowed resultstring of 0.  Simplified call to
	  Path_compute.

2002-09-27 09:41  twu

	* whats_on, util/whats_on: Added -R flag for release number.

2002-09-25 08:59  twu

	* intlist.c, intlist.h, scoremat.c, scoremat.h, src/intlist.c,
	  src/intlist.h: No longer need Intlist_T or Scoremat_T.

2002-09-25 08:48  twu

	* reader.c, reader.h, src/reader.c, src/reader.h: Added
	  Reader_pointer function.

2002-09-25 08:48  twu

	* Makefile, path.c, path.h, snap.c, src/gmap.c, src/snap.c:
	  Removing Sequence_T.	Using char * instead to represent
	  sequences.

2002-09-25 08:02  twu

	* penalties.c: Using CALLOC/FREE macros.

2002-09-25 07:57  twu

	* snap.c, src/gmap.c, src/snap.c: Inadvertent commit.  Adding
	  routines to perform nucleotide-level dynamic programming.

2002-09-25 07:57  twu

	* path.c, path.h: Premature commit.  Adding routines to analyze
	  only submatrices.

2002-09-25 07:57  twu

	* ring.c, ring.h: Removed Ring_T.  Apparently not used by other
	  seqalign files.

2002-09-25 07:57  twu

	* intlist.c, matrix.c, scoremat.c, src/intlist.c: Using CALLOC/FREE
	  macros.

2002-09-25 07:57  twu

	* Makefile: Adding files from seqalign.

2002-09-25 07:51  twu

	* intlist.c, intlist.h, src/intlist.c, src/intlist.h: Added files
	  from seqalign to do nucleotide-level dynamic programming.

2002-09-25 07:21  twu

	* get-genome.c, src/get-genome.c: Added flag for release string.
	  Changed type of positions from long to unsigned int.

2002-09-25 07:20  twu

	* offset.c, offsetdb.c, offset.h, offsetdb.h: Added datadir to
	  Offset_read_file.

2002-09-25 07:18  twu

	* match.c, result.c, src/match.c, src/result.c, match.h, result.h,
	  src/match.h, src/result.h: Added Result_path command.

2002-09-25 07:16  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c, snapgenerate.c:
	  Simplified strcpy/strcat calls to sprintf.

2002-09-25 05:10  twu

	* matrix.c, matrix.h, ring.c, ring.h, penalties.c, penalties.h,
	  scoremat.c, scoremat.h: Added to program for doing
	  nucleotide-level dynamic program.  Taken from seqalign.

2002-09-25 05:09  twu

	* path.c: Inadvertent commit.  Still editing.

2002-09-25 04:56  twu

	* path.c, path.h: Added to program for doing nucleotide-level
	  dynamic program.  Taken from seqalign.

2002-09-24 09:44  twu

	* segmentpos.c, src/segmentpos.c, segmentpos.h, snapindex.c,
	  src/gmapindex.c, src/segmentpos.h, src/snapindex.c: Added
	  superaccessions to accsegmentpos_db.

2002-09-23 02:39  twu

	* radixsort.c: Fixed syntax error when monitoring is turned off.

2002-09-23 02:21  twu

	* Makefile, radixsort.c: Added monitoring routine for radix sort.

2002-09-19 03:24  twu

	* snapgenerate.c: Removed debug line.

2002-09-19 00:57  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Added option for
	  using lowercase characters.

2002-09-18 06:49  twu

	* Makefile, snapgenerate.c: Added program snapgenerate, to create
	  text .chromosome, .contig, and .chromosome files.

2002-09-18 06:13  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Clarified the
	  variable auxfile.

2002-09-18 06:12  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Clarified the
	  variable dbroot.

2002-09-17 06:15  twu

	* oligo.c, src/oligo.c: Made comment to explain Third Degree
	  warning.

2002-09-17 06:15  twu

	* Makefile, block.c, block.h, match.c, match.h, reqpost.c,
	  reqpost.h, result.c, result.h, snap.c, src/block.c, src/block.h,
	  src/gmap.c, src/match.c, src/match.h, src/reqpost.c,
	  src/reqpost.h, src/result.c, src/result.h, src/snap.c: Made
	  changes to sample query sequence at a test interval and perform
	  dynamic programming.

2002-09-16 06:25  twu

	* endpoints.c, endpoints.h: Removed from source.

2002-09-12 11:10  twu

	* block.c, src/block.c: Changed debug flag.

2002-09-12 11:10  twu

	* Makefile: Changed C compiler flags.

2002-09-12 11:10  twu

	* snap.c, src/gmap.c, src/snap.c: Changed default directory to be
	  in /usr/seqdb2_nb.

2002-08-30 06:11  twu

	* endpoints.c, match.c, match.h, result.c, result.h, snap.c,
	  src/gmap.c, src/match.c, src/match.h, src/result.c, src/result.h,
	  src/snap.c: Made changes to facilitate garbage collection,
	  including adding a matchedp flag to results, and putting
	  singleton results into an endpoint.

2002-08-30 05:12  twu

	* block.c, src/block.c: Changed debug messages.

2002-08-30 05:11  twu

	* endpoints.c, endpoints.h: Changed print routine.  Added code for
	  query length.

2002-08-30 05:10  twu

	* snap.c, src/gmap.c, src/snap.c: Added consolidation of endpoints,
	  and ranking of those to generate a single result.

2002-08-29 10:11  twu

	* endpoints.c, endpoints.h: Added commands for sorting endpoints
	  and testing for adjacency.

2002-08-29 10:10  twu

	* reader.c, src/reader.c: Fixed test when startptr == endptr.

2002-08-29 10:09  twu

	* segmentpos.c, src/segmentpos.c, match.c, result.c, src/match.c,
	  src/result.c, oligo.c, src/oligo.c, block.c, src/block.c: Added
	  debug macros.

2002-08-29 10:08  twu

	* snap.c, src/gmap.c, src/snap.c: Implemented divide-and-conquer
	  strategy on query sequence.

2002-08-28 08:43  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Turned off
	  printing of subaccession messages.

2002-08-22 09:23  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Added timing
	  statistics.

2002-08-22 06:11  twu

	* block.c, oligo.c, src/block.c, src/oligo.c: Fixed coordinate
	  calculations.  May need to check.

2002-08-22 06:11  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Added dump
	  function.

2002-08-22 06:10  twu

	* radixsort.c, radixsort.h: Changed accessor function to get a
	  character rather than a pointer.  Fixed algorithm for case where
	  byte equals strlen.

2002-08-22 06:10  twu

	* cell.c, cell.h: Changed accessor function to get a character
	  rather than a pointer.

2002-08-22 06:09  twu

	* Makefile, rsort-check.c, rsort-test.c: Added a test and check
	  routine for radixsort.

2002-08-21 17:04  twu

	* Makefile, snapindex.c, src/gmapindex.c, src/snapindex.c: Removed
	  unnecessary files for snapindex.

2002-08-21 16:58  twu

	* Makefile, block.c, block.h, src/block.c, src/block.h,
	  endpoints.c, endpoints.h, match.c, match.h, offset.c, offsetdb.c,
	  oligo.c, oligo.h, readcirc.c, reader.c, reader.h, request.h,
	  result.c, result.h, snap.c, src/gmap.c, src/match.c, src/match.h,
	  src/oligo.c, src/oligo.h, src/reader.c, src/reader.h,
	  src/request.h, src/result.c, src/result.h, src/snap.c: Major
	  change to implement divide-and-conquer strategy.

2002-08-21 07:49  twu

	* read.c, read.h: Changed name of file from read.c to readcirc.c

2002-08-21 07:49  twu

	* block.c, block.h, endpoints.c, src/block.c, src/block.h: Partial
	  changes to implement divide-and-conquer strategy.

2002-08-21 02:18  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Improved
	  diagnostic messages.

2002-08-20 22:12  twu

	* Makefile, offset.c, offsetdb.c, radixsort.c, radixsort.h, read.c,
	  readcirc.c, segmentpos.c, snapindex.c, src/gmapindex.c,
	  src/segmentpos.c, src/snapindex.c: Fixed minor compiler warnings.

2002-08-20 21:54  twu

	* cell.c: Using pointers rather than lists to store multiple
	  positions for an oligo.  Fixed quicksort compare function
	  accordingly.

2002-08-20 21:53  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Using pointers
	  rather than lists to store multiple positions for an oligo.

2002-08-20 21:53  twu

	* radixsort.c: Added small speed hacks.

2002-08-20 21:52  twu

	* Makefile: Added quicksort as an option.

2002-08-20 21:15  twu

	* Makefile, cell.c, cell.h, radixsort.c, radixsort.h, snapindex.c,
	  src/gmapindex.c, src/snapindex.c: Added radix sort as a
	  replacement for quicksort.

2002-08-20 08:56  twu

	* oligo.c, src/oligo.c: Fixed key_size for partial bytes.

2002-08-20 06:52  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Changed location
	  of oligo file to be in dbenv directory, not a subdirectory.

2002-08-15 09:35  twu

	* Makefile, block.c, block.h, oligo.c, oligo.h, request.c,
	  src/block.c, src/block.h, src/oligo.c, src/oligo.h,
	  src/request.c, request.h, snap-withenv.c, snap.c, snapindex.c,
	  src/gmap.c, src/gmapindex.c, src/request.h, src/snap.c,
	  src/snapindex.c: Made changes to accommodate sizes less than
	  32-mers.

2002-08-15 07:35  twu

	* offset.c, offsetdb.c, match.c, match.h, offset.h, offsetdb.h,
	  result.c, result.h, snap.c, src/gmap.c, src/match.c, src/match.h,
	  src/result.c, src/result.h, src/snap.c: Added ability to read
	  chromosome information from file, but not done by default right
	  now.

2002-08-11 05:22  twu

	* Makefile, block.c, block.h, src/block.c, src/block.h, dpentry.c,
	  dpentry.h, endpoints.c, endpoints.h, match.c, match.h, result.c,
	  result.h, snap.c, src/gmap.c, src/match.c, src/match.h,
	  src/result.c, src/result.h, src/snap.c: Changed algorithm to work
	  inward from both ends and find a single match.

2002-08-10 10:46  twu

	* Makefile, snapindex.c, src/gmapindex.c, src/snapindex.c: Fixed
	  program to handle cases where interval is less than size.

2002-07-19 05:00  twu

	* segmentpos.c, src/segmentpos.c: Changed type of querylen.

2002-07-19 05:00  twu

	* whats_on, util/whats_on: Changed suffix for db filenames.

2002-07-19 04:59  twu

	* iit-read.c, iit.c, src/iit-read.c, interval-read.c, interval.c,
	  src/interval.c, interval-read.h, interval.h, src/interval.h:
	  Changed binary storage format to be a single file.

2002-07-19 04:57  twu

	* get-genome.c, src/get-genome.c: Changed input format to accept a
	  single string.

2002-07-13 01:43  twu

	* iit_get.c, src/iit_get.c: Added ability to query symbolic db.

2002-07-12 12:09  twu

	* iit_get.c, src/iit_get.c: Fixed bugs in the algorithm.

2002-07-12 10:14  twu

	* iit_get.c, src/iit_get.c: Allowed user to specify a single point,
	  rather than an interval.

2002-07-12 10:14  twu

	* iit_store.c, src/iit_store.c: Added an output message when
	  Berkeley DB file is done.

2002-07-12 08:16  twu

	* iit_get.c, iit_store.c, src/iit_get.c, src/iit_store.c:
	  Integrated interval tree into db_load/retrieve_endpoints.

2002-07-12 05:47  twu

	* Makefile, basic.h, iit-read.c, iit.c, interval-read.c,
	  interval-read.h, interval.c, interval.h, src/iit-read.c,
	  src/interval.c, src/interval.h: Rewrote interval tree to handle
	  interval queries and to write tree to and read tree from files.

2002-07-11 08:19  twu

	* basic.h, iit-read.c, iit.c, src/iit-read.c: Added code for
	  integer interval trees from Edelsbrunner's alpha shapes.

2002-07-11 05:22  twu

	* get-genome.c, src/get-genome.c: Added ability to convert a single
	  coordinate.

2002-07-11 05:20  twu

	* prb.c: Fixed minor typos.

2002-07-11 05:19  twu

	* prb.c, prb.h: Revised format and separated interface from
	  implementation.

2002-07-11 03:02  twu

	* prb.c, prb.h: Added routines for red-black trees with parent
	  pointers from libavl 2.0

2002-07-10 14:20  twu

	* dpentry.c: Changed criterion to consider query coverage.

2002-07-10 14:19  twu

	* endpoints.c: Fixed problem with negative relative positions.

2002-07-09 15:10  twu

	* endpoints.c, endpoints.h, snap.c, src/gmap.c, src/snap.c: Revised
	  output format of SNAP.  Coordinates are now given for each
	  accession.

2002-07-09 12:46  twu

	* offset.c, offset.h, offsetdb.c, offsetdb.h, snap.c, src/gmap.c,
	  src/snap.c: Revised chromosome dump procedure to print lengths as
	  well as offsets.

2002-07-09 11:28  twu

	* Makefile, add-chrpos-to-endpoints.c: Added program for adding
	  chromosomal position to endpoints.

2002-07-09 08:38  twu

	* whats_on, util/whats_on: Modified program to work with new
	  version of SNAP.

2002-07-08 11:11  twu

	* dpentry.c, match.c, match.h, result.c, result.h, snap.c,
	  src/gmap.c, src/match.c, src/match.h, src/result.c, src/result.h,
	  src/snap.c: Restored nleads as a criterion in dynamic
	  programming.	Added features to help with debugging.

2002-07-08 10:28  twu

	* Makefile, get-genome.c, src/get-genome.c: Freed get-genome from
	  using BerkeleyDB databases, which are too slow to open.

2002-07-08 06:33  twu

	* get-genome.c, src/get-genome.c: Added ability to report
	  coordinates.

2002-07-08 05:09  twu

	* iit_get.c, src/iit_get.c: Added check for zero matches.

2002-07-08 04:49  twu

	* whats_on, util/whats_on: Preliminary changes (inadvertent
	  checkin).

2002-07-08 04:49  twu

	* Makefile, get-genome.c, src/get-genome.c: Created get-genome
	  program.

2002-07-08 03:44  twu

	* accpos.c: Added offset for chromosomes.

2002-07-08 03:26  twu

	* accpos.c, database.c, database.h, snap.c, src/gmap.c, src/snap.c,
	  snapindex.c, src/gmapindex.c, src/snapindex.c: Changed location
	  of data files.

2002-07-07 06:54  twu

	* iit_get.c, src/iit_get.c: Fixed bug with testing dumpp.

2002-07-06 01:59  twu

	* endpoints.c, endpoints.h, match.c, result.c, src/match.c,
	  src/result.c: Added check for boomerang paths, where the genomic
	  length is 0.

2002-07-05 14:10  twu

	* whats_on, util/whats_on: Added whats_on from ../snap.

2002-07-05 13:59  twu

	* spidey_compress.pl, util/spidey_compress.pl: Added meta-level
	  compression.

2002-07-05 08:40  twu

	* spidey_compress.pl, util/spidey_compress.pl: Added
	  spidey_compress.pl from ../snap.

2002-07-05 05:57  twu

	* iit_get.c, src/iit_get.c: Added dump utility.

2002-07-05 04:32  twu

	* iit_get.c, iit_store.c, src/iit_get.c, src/iit_store.c: Added
	  programs for storing and retrieving records based on endpoints.

2002-07-03 17:32  twu

	* sim4_uncompress.pl, util/sim4_uncompress.pl: Added retrieval
	  function for get-genome.

2002-07-03 16:58  twu

	* sim4_compress.pl, sim4_uncompress.pl, util/sim4_compress.pl,
	  util/sim4_uncompress.pl: Added further compression by counting
	  repeated tokens.

2002-07-03 16:22  twu

	* sim4_compress.pl, sim4_uncompress.pl, util/sim4_compress.pl,
	  util/sim4_uncompress.pl: Added sim4 compression/uncompression
	  routines from snap CVS archive.

2002-07-03 16:10  twu

	* dpentry.c, match.c, result.c, src/match.c, src/result.c: Changed
	  from using slopes (quotients) to intron measurements
	  (differences).

2002-07-03 06:40  twu

	* endpoints.c, snap.c, src/gmap.c, src/snap.c: Changed output
	  slightly, e.g., en-dash for number ranges.

2002-07-03 05:11  twu

	* Makefile, accpos.c: Created program accpos, for finding genomic
	  position of accessions.

2002-07-03 05:11  twu

	* segmentpos.c, segmentpos.h, src/segmentpos.c, src/segmentpos.h:
	  Added procedure for finding partially matching accessions.

2002-07-03 05:10  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Made creation of
	  aux-only database faster.

2002-07-03 03:33  twu

	* snap.c, src/gmap.c, src/snap.c: Fixed small bug in error message.

2002-07-03 03:33  twu

	* segmentpos.c, segmentpos.h, src/segmentpos.c, src/segmentpos.h:
	  Made Segmentpos_print extern.

2002-07-03 03:32  twu

	* database.c: Changed accsegmentpos_db from hash to B-tree.

2002-07-03 03:06  twu

	* database.c, database.h, snap.c, snapindex.c, src/gmap.c,
	  src/gmapindex.c, src/snap.c, src/snapindex.c: Merged two database
	  procedures.

2002-07-03 03:06  twu

	* segmentpos.c, segmentpos.h, src/segmentpos.c, src/segmentpos.h:
	  Added procedure for reading from accsegmentpos_db.

2002-07-03 02:45  twu

	* Makefile, cell.c, cell.h, database.c, database.h, endpoints.c,
	  endpoints.h, segmentpos.c, segmentpos.h, snap.c, snapindex.c,
	  src/gmap.c, src/gmapindex.c, src/segmentpos.c, src/segmentpos.h,
	  src/snap.c, src/snapindex.c: Added another database, from
	  accession name to segmentpos, and renamed databases.

2002-07-02 10:07  twu

	* Makefile, block.c, block.h, snap.c, src/block.c, src/block.h,
	  src/gmap.c, src/snap.c: Added specification for minimum
	  separation between leads.

2002-07-02 04:40  twu

	* endpoints.c, endpoints.h, snap.c, src/gmap.c, src/snap.c: Changed
	  to 1-based coordinates as default.

2002-07-02 04:40  twu

	* Makefile: Removed segmentpos dump flag from db.test

2002-07-02 04:12  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Removed segment
	  dump, because it can be performed by snap.

2002-07-02 04:12  twu

	* snap.c, src/gmap.c, src/snap.c: Added several command-line
	  options.

2002-07-02 04:11  twu

	* segmentpos.c, segmentpos.h, src/segmentpos.c, src/segmentpos.h:
	  Enhanced dump procedure to report absolute genomic positions.

2002-07-02 04:11  twu

	* match.c, result.c, src/match.c, src/result.c, match.h, result.h,
	  src/match.h, src/result.h: Storing signed genome_coverage into
	  dpentry and checking for impossible slopes (< 0.9).

2002-07-02 04:00  twu

	* offset.c, offset.h, offsetdb.c, offsetdb.h: Added dump procedure.

2002-07-02 03:59  twu

	* endpoints.c: Added printing of subaccessions for Celera genome.
	  Added commas to output of positions.	Changed dominated function
	  to look for any overlap instead of complete coverage.

2002-07-02 03:57  twu

	* Makefile, dpentry.c, dpentry.h: Changed comparison function to
	  use slopes.

2002-07-02 03:56  twu

	* chrnum.c, src/chrnum.c: Added check for uninitialized chromosome.

2002-07-01 09:26  twu

	* block.h, buffer-thread-attempt.c, src/block.h,
	  buffer-thread-attempt.h, buffer.c, buffer.h, dbentry.c,
	  dbentry.h, entry.c, entry.h, hits.c, hits.h, oligo.c, sort.c,
	  sort.h, table.c, table.h, src/oligo.c, src/table.c, src/table.h:
	  Removed unused files.

2002-07-01 09:15  twu

	* Makefile, block.c, block.h, database.c, database.h, endpoints.c,
	  endpoints.h, hash-oligos.c, hit.c, hit.h, oligo.c, oligo.h,
	  request.c, src/block.c, src/block.h, src/oligo.c, src/oligo.h,
	  src/request.c, match.c, match.h, request.h, result.c, result.h,
	  scan.c, scan.h, segmentpos.c, snap.c, snapindex.c, src/gmap.c,
	  src/gmapindex.c, src/match.c, src/match.h, src/request.h,
	  src/result.c, src/result.h, src/segmentpos.c, src/snap.c,
	  src/snapindex.c: Changed oligo_db from BerkeleyDB to PureDB.
	  Created object for endpoints.  Removed unused files.

2002-06-29 14:23  twu

	* segmentpos.c, src/segmentpos.c, segmentpos.h, snap.c, src/gmap.c,
	  src/segmentpos.h, src/snap.c: Added genomic position to the
	  output.

2002-06-29 04:50  twu

	* match.c, result.c, snap.c, src/gmap.c, src/match.c, src/result.c,
	  src/snap.c: Fixed memory leaks.

2002-06-29 04:44  twu

	* block.c, src/block.c, block.h, dpentry.c, dpentry.h, match.c,
	  match.h, request.c, request.h, result.c, result.h, snap.c,
	  src/block.h, src/gmap.c, src/match.c, src/match.h, src/request.c,
	  src/request.h, src/result.c, src/result.h, src/snap.c: Added
	  minimum spanning tree.  Version appears to work well.

2002-06-28 23:15  twu

	* Makefile, block.c, block.h, src/block.c, src/block.h, dpentry.c,
	  dpentry.h, match.c, match.h, request.c, request.h, result.c,
	  result.h, snap.c, src/gmap.c, src/match.c, src/match.h,
	  src/request.c, src/request.h, src/result.c, src/result.h,
	  src/snap.c: Early version of dynamic programming that stores H
	  best paths at each hit.

2002-06-28 09:29  twu

	* match.c, match.h, result.c, result.h, segmentpos.c, snap.c,
	  src/gmap.c, src/match.c, src/match.h, src/result.c, src/result.h,
	  src/segmentpos.c, src/snap.c: Added simple dynamic programming
	  and best pair techniques.

2002-06-27 23:07  twu

	* Makefile, block.c, block.h, database.c, src/block.c, src/block.h,
	  database.h, match.c, match.h, oligo.c, oligo.h, reqpost.c,
	  request.c, request.h, result.c, result.h, snap.c, snapindex.c,
	  src/gmap.c, src/gmapindex.c, src/match.c, src/match.h,
	  src/oligo.c, src/oligo.h, src/reqpost.c, src/request.c,
	  src/request.h, src/result.c, src/result.h, src/snap.c,
	  src/snapindex.c: Implemented working version of snap that uses
	  multiple oligo_dbs with requests and strings results together
	  from 5' and 3' ends.

2002-06-27 23:05  twu

	* commafmt.c, commafmt.h: Added source code for adding commas to
	  numbers.

2002-06-25 04:50  twu

	* Makefile: Added specification of directory for dbenv.

2002-06-25 04:40  twu

	* database.c, snapindex.c, src/gmapindex.c, src/snapindex.c: Added
	  provisions for transactions, to try to speed up build of
	  database.

2002-05-29 03:56  twu

	* snapindex.c, src/gmapindex.c, src/snapindex.c: Allowed the user
	  to specify a directory for the BerkeleyDB environment.

2002-05-27 15:34  twu

	* Makefile, segmentpos.c, snapindex.c, src/gmapindex.c,
	  src/segmentpos.c, src/snapindex.c: Added specification of
	  segmentfile as flag -g.

2002-05-27 15:29  twu

	* Makefile, database.c, database.h, snapindex.c, src/gmapindex.c,
	  src/snapindex.c: Removed genome_db and delta_db from snapindex.

2002-05-27 15:18  twu

	* Makefile, segmentpos.c, segmentpos.h, snapindex.c,
	  src/gmapindex.c, src/segmentpos.c, src/segmentpos.h,
	  src/snapindex.c: Added ability to dump segments (in order) from
	  segmentpos_db

2002-05-27 14:24  twu

	* Makefile: Changed flags for C compiler.

2002-05-27 14:24  twu

	* segmentpos.c, src/segmentpos.c: Added check to get previous
	  segment only in some cases.

2002-05-22 09:18  twu

	* Makefile, oligo.c, oligo.h, read.c, read.h, readcirc.c,
	  readcirc.h, scan.c, scan.h, segmentpos.c, segmentpos.h, snap.c,
	  src/gmap.c, src/oligo.c, src/oligo.h, src/segmentpos.c,
	  src/segmentpos.h, src/snap.c: Working version of snap using a
	  scan of genomic and delta information.

2002-05-21 10:25  twu

	* Makefile, cell.c, cell.h, database.c, database.h, hit.c, hit.h,
	  offset.c, offset.h, offsetdb.c, offsetdb.h, oligo.c, oligo.h,
	  scan.c, scan.h, snap.c, snapindex.c, table.c, src/gmap.c,
	  src/gmapindex.c, src/oligo.c, src/oligo.h, src/snap.c,
	  src/snapindex.c, src/table.c, table.h, src/table.h: Made changes
	  to store delta position of genomic oligos and to store oligos of
	  query sequence.

2002-05-08 05:17  twu

	* Makefile, database.c, database.h, hash-oligos.c, snap.c,
	  snapindex.c, src/gmap.c, src/gmapindex.c, src/snap.c,
	  src/snapindex.c: Consolidated sample-oligos and hash-oligos into
	  snapindex.  Specified oligo dbtype by using Berkeley DB
	  constants.

2002-05-03 09:22  twu

	* Makefile, cell.c, cell.h, database.c, database.h, hit.c, read.c,
	  readcirc.c, sample-oligos.c: Separated database commands for
	  oligos from the other database (aux).

2002-04-26 08:47  twu

	* Makefile, hit.c, oligo.c, read.c, readcirc.c, snap.c, src/gmap.c,
	  src/oligo.c, src/snap.c: Removed environment.  Began
	  implementation of dynamic programming.

2002-04-26 05:51  twu

	* Makefile, chrnum.c, chrnum.h, database.c, database.h,
	  hash-oligos.c, hit.c, hit.h, offset.c, offset.h, offsetdb.c,
	  offsetdb.h, oligo.c, oligo.h, read.c, read.h, readcirc.c,
	  readcirc.h, snap.c, src/chrnum.c, src/chrnum.h, src/gmap.c,
	  src/oligo.c, src/oligo.h, src/snap.c: Re-implementation of SNAP
	  using new database created by hash-oligos.

2002-04-24 08:21  twu

	* segmentpos.c, segmentpos.h, src/segmentpos.c, src/segmentpos.h:
	  Handled problems with chromosome string to integer conversions.

2002-04-24 08:21  twu

	* hash-oligos.c: Handled problems with chromosome string to integer
	  conversions.	Rearranged calls to db->open so that each db is
	  opened only once.

2002-04-24 06:35  twu

	* Makefile, btree.c, btree.h, hash-oligos.c, hash.c, hash.h,
	  oligo.c, oligo.h, src/oligo.c, src/oligo.h: Consolidated code
	  into fewer files.

2002-04-24 05:02  twu

	* Makefile: Changed CFLAGS to optimize speed.

2002-04-24 05:02  twu

	* cell.h: Matched up .h file with .c file.

2002-04-24 04:58  twu

	* Makefile, genomicpos.c, genomicpos.h, hash-oligos.c,
	  segmentpos.c, segmentpos.h, src/genomicpos.c, src/genomicpos.h,
	  src/segmentpos.c, src/segmentpos.h: Now storing genomic locations
	  as global positions, which require keeping track of chromosomal
	  offsets.

2002-04-24 01:04  twu

	* Makefile, btree.c, btree.h, cell.c, cell.h, entry.c, entry.h,
	  genomicpos.c, genomicpos.h, hash-oligos.c, sample-oligos.c,
	  src/genomicpos.c, src/genomicpos.h: Major change to allow
	  B-trees, to avoid storing adjacent oligos, to store genomic
	  positions, and to write oligos in binary format.

2002-04-22 07:50  twu

	* Makefile, assert.c, block.c, buffer-thread-attempt.c, buffer.c,
	  cksum-fa.c, cksum.c, dbentry.c, entry.c, except.c, hash-oligos.c,
	  hash-test.c, hash.c, hits.c, list.c, match.c, mem.c, oligo.c,
	  read.c, readcirc.c, reqpost.c, request.c, result.c, src/assert.c,
	  src/block.c, src/except.c, src/list.c, src/match.c, src/mem.c,
	  src/oligo.c, src/reqpost.c, src/request.c, src/result.c,
	  assert.h, block.h, bool.h, buffer-thread-attempt.h, buffer.h,
	  dbentry.h, entry.h, except.h, hash.h, hits.h, list.h, match.h,
	  mem.h, oligo.h, read.h, readcirc.h, reqpost.h, request.h,
	  result.h, sample-oligos.c, snap-withenv.c, snap.c, sort.c,
	  sort.h, src/assert.h, src/block.h, src/bool.h, src/except.h,
	  src/gmap.c, src/list.h, src/match.h, src/mem.h, src/oligo.h,
	  src/reqpost.h, src/request.h, src/result.h, src/snap.c: Initial
	  import into CVS.

2002-04-22 07:50  twu

	* Makefile, assert.c, block.c, buffer-thread-attempt.c, buffer.c,
	  cksum-fa.c, cksum.c, dbentry.c, entry.c, except.c, hash-oligos.c,
	  hash-test.c, hash.c, hits.c, list.c, match.c, mem.c, oligo.c,
	  read.c, readcirc.c, reqpost.c, request.c, result.c, src/assert.c,
	  src/block.c, src/except.c, src/list.c, src/match.c, src/mem.c,
	  src/oligo.c, src/reqpost.c, src/request.c, src/result.c,
	  assert.h, block.h, bool.h, buffer-thread-attempt.h, buffer.h,
	  dbentry.h, entry.h, except.h, hash.h, hits.h, list.h, match.h,
	  mem.h, oligo.h, read.h, readcirc.h, reqpost.h, request.h,
	  result.h, sample-oligos.c, snap-withenv.c, snap.c, sort.c,
	  sort.h, src/assert.h, src/block.h, src/bool.h, src/except.h,
	  src/gmap.c, src/list.h, src/match.h, src/mem.h, src/oligo.h,
	  src/reqpost.h, src/request.h, src/result.h, src/snap.c: Initial
	  revision