File: ChangeLog

package info (click to toggle)
maq 0.7.1-3
links: PTS, VCS
area: main
in suites: squeeze
size: 1,360 kB
ctags: 993
sloc: cpp: 5,025; ansic: 3,329; sh: 3,282; perl: 2,547; makefile: 27
file content (4187 lines) | stat: -rw-r--r-- 144,967 bytes
parent folder | download | duplicates (5)
------------------------------------------------------------------------
r666 | lh3lh3 | 2008-09-21 20:31:54 +0100 (Sun, 21 Sep 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/eland2maq.cc

updated novo2maq

------------------------------------------------------------------------
r665 | lh3lh3 | 2008-09-17 13:09:01 +0100 (Wed, 17 Sep 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl

 * fq_all2std.pl-0.1.7
 * convert fastq to .seq+.qual format

------------------------------------------------------------------------
r662 | lh3lh3 | 2008-09-08 14:09:02 +0100 (Mon, 08 Sep 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/simulate.c

 * maq-0.6.8-5
 * fixed a flaw in simulate.c

------------------------------------------------------------------------
r661 | lh3lh3 | 2008-09-04 22:44:59 +0100 (Thu, 04 Sep 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/dword.hh
   M /branches/lh3/maq/eland2maq.cc
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/maqmap.h
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.8-4
 * support long reads and this is the default. It works on toy examples.
   Further testing is needed.
 * Fixed a bug in novo2maq

------------------------------------------------------------------------
r660 | lh3lh3 | 2008-09-04 20:01:44 +0100 (Thu, 04 Sep 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/stdaln.c
   M /branches/lh3/maq/stdaln.h

 * maq-0.6.8-3
 * apparently fixed a segfault in indelpe
 * reduce debugging information in indelpe

------------------------------------------------------------------------
r659 | lh3lh3 | 2008-08-27 09:25:33 +0100 (Wed, 27 Aug 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/bfa.c
   M /branches/lh3/maq/bfa.h
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc

 * maq-0.6.8-2
 * map: better stats
 * indelpe: better boundary check, but it still segfaults

------------------------------------------------------------------------
r657 | lh3lh3 | 2008-08-19 09:53:26 +0100 (Tue, 19 Aug 2008) | 9 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/eland2maq.cc
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/scripts/asub
   M /branches/lh3/maq/scripts/fq_all2std.pl

 * maq-0.6.8-1
 * map: added -W to disable Smith-Waterman alignment. It segfaults for
   Aylwyn's alignment and I have not figured out the cause.
 * Added novo2map to convert novocraft alignment to .map, provided by Colin.
 * fq_all2std.pl: added std2sol to convert Sanger fastq to Solexa fastq
 * asub-0.1.5: added -M to set maximum memory on Sanger's farm; added -n
   to specify the maximum cores for parallel jobs


------------------------------------------------------------------------
r651 | lh3lh3 | 2008-07-27 17:07:44 +0100 (Sun, 27 Jul 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod

Release maq-0.6.8

------------------------------------------------------------------------
r648 | lh3lh3 | 2008-07-27 13:38:43 +0100 (Sun, 27 Jul 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/maq.pod

update man page

------------------------------------------------------------------------
r647 | lh3lh3 | 2008-07-27 00:19:13 +0100 (Sun, 27 Jul 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac

 * maq-0.6.8-9
 * fixed a potential compiling error in assopt.c

------------------------------------------------------------------------
r646 | lh3lh3 | 2008-07-24 15:46:31 +0100 (Thu, 24 Jul 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/COPYING
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc

 * maq-0.6.7-8
 * fixed a potential bug in indel_pe.cc
 * change COPYING to GPLv3

------------------------------------------------------------------------
r645 | lh3lh3 | 2008-07-24 15:45:47 +0100 (Thu, 24 Jul 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_plot.pl

use /usr/bin/perl instead of /usr/local/bin/perl

------------------------------------------------------------------------
r644 | lh3lh3 | 2008-07-24 15:45:08 +0100 (Thu, 24 Jul 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq_sanger.pl-0.1.16
 * support .fq 

------------------------------------------------------------------------
r643 | lh3lh3 | 2008-07-16 10:08:41 +0100 (Wed, 16 Jul 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/mapcheck.cc

 * maq-0.6.7-7
 * mapcheck: fixed a bug caused by previous modification

------------------------------------------------------------------------
r642 | lh3lh3 | 2008-07-16 09:51:40 +0100 (Wed, 16 Jul 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/mapcheck.cc

 * maq-0.6.7-6
 * mapcheck: fixed a bug in the last modification

------------------------------------------------------------------------
r641 | lh3lh3 | 2008-07-15 15:16:52 +0100 (Tue, 15 Jul 2008) | 7 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/scripts/maq_sanger.pl
   M /branches/lh3/maq/scripts/paf_utils.pl

 * paf_utils.pl-0.3.2
 * partially support novoalign/novopaired
 * maq_sanger.pl-0.1.15
 * dump unmapped reads
 * maq-0.6.7-5
 * filter out know polymorphic positions

------------------------------------------------------------------------
r640 | lh3lh3 | 2008-06-29 09:58:27 +0100 (Sun, 29 Jun 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.7-4
 * map: only dump unmapped reads

------------------------------------------------------------------------
r637 | lh3lh3 | 2008-06-26 13:57:37 +0100 (Thu, 26 Jun 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/glfgen.cc

 * maq-0.6.7-3
 * fixed a memory leak

------------------------------------------------------------------------
r635 | lh3lh3 | 2008-06-25 20:36:31 +0100 (Wed, 25 Jun 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac

 * maq-0.6.7-2
 * assemble: change default -t to 0.85

------------------------------------------------------------------------
r634 | lh3lh3 | 2008-06-25 17:02:41 +0100 (Wed, 25 Jun 2008) | 2 lines
Changed paths:
   A /branches/lh3/glf
   A /branches/lh3/glf/Makefile
   A /branches/lh3/glf/glf.c
   A /branches/lh3/glf/glf.h
   A /branches/lh3/glf/glf_main.c
   A /branches/lh3/glf/izlib
   A /branches/lh3/glf/izlib/Makefile
   A /branches/lh3/glf/izlib/adler32.c
   A /branches/lh3/glf/izlib/compress.c
   A /branches/lh3/glf/izlib/crc32.c
   A /branches/lh3/glf/izlib/crc32.h
   A /branches/lh3/glf/izlib/deflate.c
   A /branches/lh3/glf/izlib/deflate.h
   A /branches/lh3/glf/izlib/gzio.c
   A /branches/lh3/glf/izlib/infback.c
   A /branches/lh3/glf/izlib/inffast.c
   A /branches/lh3/glf/izlib/inffast.h
   A /branches/lh3/glf/izlib/inffixed.h
   A /branches/lh3/glf/izlib/inflate.c
   A /branches/lh3/glf/izlib/inflate.h
   A /branches/lh3/glf/izlib/inftrees.c
   A /branches/lh3/glf/izlib/inftrees.h
   A /branches/lh3/glf/izlib/izio.c
   A /branches/lh3/glf/izlib/izlib.h
   A /branches/lh3/glf/izlib/trees.c
   A /branches/lh3/glf/izlib/trees.h
   A /branches/lh3/glf/izlib/uncompr.c
   A /branches/lh3/glf/izlib/zconf.h
   A /branches/lh3/glf/izlib/zindex.c
   A /branches/lh3/glf/izlib/zlib.h
   A /branches/lh3/glf/izlib/zran.c
   A /branches/lh3/glf/izlib/zutil.c
   A /branches/lh3/glf/izlib/zutil.h
   A /branches/lh3/glf/stdhash
   A /branches/lh3/glf/stdhash/Makefile
   A /branches/lh3/glf/stdhash/simple_test.c
   A /branches/lh3/glf/stdhash/stdhash.hh
   A /branches/lh3/glf/stdhash/stdhash_test.cc
   A /branches/lh3/glf/stdhash/stdhashc.cc
   A /branches/lh3/glf/stdhash/stdhashc.h
   M /branches/lh3/maq/configure.ac

utilities for .glz format

------------------------------------------------------------------------
r633 | lh3lh3 | 2008-06-25 15:20:49 +0100 (Wed, 25 Jun 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   A /branches/lh3/maq/glf.h
   A /branches/lh3/maq/glfgen.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h

 * maq-0.6.7-1
 * add glfgen
 * fixed a bug in assemble
 * the default parameters should be updated due to that bug!!!

------------------------------------------------------------------------
r630 | lh3lh3 | 2008-06-23 15:03:02 +0100 (Mon, 23 Jun 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/maq.pod

Release maq-0.6.7

------------------------------------------------------------------------
r629 | lh3lh3 | 2008-06-23 14:48:36 +0100 (Mon, 23 Jun 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/maq.pod

 * update ChangeLog and maq.pod
 * prepare to release maq-0.6.7

------------------------------------------------------------------------
r628 | lh3lh3 | 2008-06-23 14:47:15 +0100 (Mon, 23 Jun 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.4.7
 * SNPfilter: also filter on consensus quality
 * easyrun: change for SNPfilter. cns.filter.snp is now a symbolic link to
   cns.final.snp
 * easyrun: do not apply splitread by default

------------------------------------------------------------------------
r627 | lh3lh3 | 2008-06-23 14:45:15 +0100 (Mon, 23 Jun 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq_eval.pl-0.1.11
 * geno: print lines where genotyping calls a hom, but maq calls differently

------------------------------------------------------------------------
r626 | lh3lh3 | 2008-06-17 15:54:06 +0100 (Tue, 17 Jun 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   A /branches/lh3/maq/break_pair.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/mapcheck.cc

 * maq-0.6.6-14
 * add breakpair: for David's script
 * mapcheck: output the count of qualities - also for David's script

------------------------------------------------------------------------
r625 | lh3lh3 | 2008-06-17 14:46:26 +0100 (Tue, 17 Jun 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.4.6
 * SNPfilter: improve indel filter, as maq always puts the indel at the
   beginning of a homopolymer run
 * easyrun: allow to skip splitread indel detection

------------------------------------------------------------------------
r624 | lh3lh3 | 2008-06-17 14:43:52 +0100 (Tue, 17 Jun 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq_eval.pl-0.1.10
 * improve the evaluation of indelpe

------------------------------------------------------------------------
r623 | lh3lh3 | 2008-06-06 14:05:20 +0100 (Fri, 06 Jun 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.4.4
 * indelpe: fix a bug in parsing command-line options
 * indelpe: change the default options

------------------------------------------------------------------------
r622 | lh3lh3 | 2008-06-05 20:54:14 +0100 (Thu, 05 Jun 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   M /branches/lh3/maq/indel_call.cc
   M /branches/lh3/maq/merge.cc
   M /branches/lh3/maq/scripts/maq.pl

 * maq-0.6.6-13
 * indelpe: output number of mismatches of reads mapped without indels
 * maq.pl-0.4.3
 * filter based on this information

------------------------------------------------------------------------
r621 | lh3lh3 | 2008-05-30 00:04:55 +0100 (Fri, 30 May 2008) | 7 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   M /branches/lh3/maq/indel_call.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/merge.cc
   M /branches/lh3/maq/scripts/maq.pl

 * maq-0.6.6-11
 * indelpe: output indel bases
 * mapmerge: detect corrupted .map files
 * add mapvalidate: detect correpted .map files
 * maq.pl
 * add indelpe: correct counts for homopolymer runs

------------------------------------------------------------------------
r620 | lh3lh3 | 2008-05-24 10:06:20 +0100 (Sat, 24 May 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   M /branches/lh3/maq/indel_call.cc
   M /branches/lh3/maq/indel_pe.cc

 * maq-0.6.6-10
 * fixed bug in map: positions for insertions are shifted by 1bp
 * output more information about indel
 * have NOT tested yet

------------------------------------------------------------------------
r619 | lh3lh3 | 2008-05-23 12:40:03 +0100 (Fri, 23 May 2008) | 7 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/sort_mapping.cc
   M /branches/lh3/maq/submap.c

 * maq-0.6.6-9
 * also put unmapped reads in a pair in the alignment file. it will get
   a flag 192
 * fix a bug in submap
 * map: give an error when -n 0 is used


------------------------------------------------------------------------
r618 | lh3lh3 | 2008-05-21 15:14:57 +0100 (Wed, 21 May 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.4.2
 * change filters for splitread indels

------------------------------------------------------------------------
r617 | lh3lh3 | 2008-05-19 11:58:17 +0100 (Mon, 19 May 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/scripts/maq_sanger.pl
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.6-8
 * map: fix a bug for alignment on Illumina long insert-size library
 * maq_sanger.pl-0.1.14
 * support long insert library

------------------------------------------------------------------------
r616 | lh3lh3 | 2008-05-18 23:56:48 +0100 (Sun, 18 May 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.6-7
 * map: option to output pair-2-diff flag (for splitread ONLY)

------------------------------------------------------------------------
r615 | lh3lh3 | 2008-05-18 23:55:09 +0100 (Sun, 18 May 2008) | 7 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.4.1
 * easyrun: more options for parameter tuning
 * SNPfilter: filter for splitread indels
 * SNPfilter: change default indel window to 5
 * SNPfilter: remove the hidden filter
 * easyrun: filter for splitread indels

------------------------------------------------------------------------
r614 | lh3lh3 | 2008-05-18 18:31:38 +0100 (Sun, 18 May 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.4.0
 * splitread: find short indels by SplitRead (VERY SLOW)

------------------------------------------------------------------------
r613 | lh3lh3 | 2008-05-17 16:00:09 +0100 (Sat, 17 May 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/scripts/maq.pl

 * maq-0.6.6-6
 * reduce the minimum read length to 12

------------------------------------------------------------------------
r612 | lh3lh3 | 2008-05-17 13:56:45 +0100 (Sat, 17 May 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.13
 * sv: fix a bug

------------------------------------------------------------------------
r611 | lh3lh3 | 2008-05-14 22:37:24 +0100 (Wed, 14 May 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/scripts/maq.pl
   M /branches/lh3/maq/sort_mapping.cc

 * maq.pl-0.3.13
 * change default quality cut-off to 40
 * maq-0.6.6-5
 * map: long insert-size seems to work

------------------------------------------------------------------------
r610 | lh3lh3 | 2008-05-14 17:11:00 +0100 (Wed, 14 May 2008) | 13 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/scripts/maq.pl

 * maq-0.6.6-4
 * assemble: fix a minor bug since 0.6.4, which may affect a small fraction
   of SNP calls.
 * assemble: a tiny fix for approximation
 * assemble: add independent model, but it does not work well at all (maybe
   another bug?).
 * assemble: output debugging information
 * cns2snp/cns2view: output base2, base3 and qual2
 * map: long insert-size codes have not been tested at all
 * maq.pl-0.3.12
 * easyrun: add more options
 * easyrun: change consensus quality filter to (I think) the correct way

------------------------------------------------------------------------
r609 | lh3lh3 | 2008-05-11 19:57:27 +0100 (Sun, 11 May 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.6-3
 * initial codes for Illumina long insert library, not tested at all

------------------------------------------------------------------------
r608 | lh3lh3 | 2008-05-05 21:32:46 +0100 (Mon, 05 May 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac

 * maq-0.6.6-2
 * initial codes for pooled sample, which apparently work but not tested.

------------------------------------------------------------------------
r607 | lh3lh3 | 2008-05-01 10:55:49 +0100 (Thu, 01 May 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl
   M /branches/lh3/maq/scripts/maq_post.pl

 * maq_eval.pl-0.1.8
 * fix a bug when length >2Gbp
 * maq_post.pl-0.1.2
 * fix a bug when hapmap2.snp is not present

------------------------------------------------------------------------
r606 | lh3lh3 | 2008-04-30 14:04:41 +0100 (Wed, 30 Apr 2008) | 3 lines
Changed paths:
   A /branches/lh3/maq/scripts/maq_post.pl
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * add maq_post.pl: post process the maq alignment (for Sanger only)
 * remove aln.map.touch in the end

------------------------------------------------------------------------
r601 | lh3lh3 | 2008-04-27 19:52:12 +0100 (Sun, 27 Apr 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/FUTURES
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod

Release maq-0.6.6

------------------------------------------------------------------------
r600 | lh3lh3 | 2008-04-27 19:24:25 +0100 (Sun, 27 Apr 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/match.cc

 * maq-0.6.5-3
 * map: fix a bug in dumping multi-hit
 * add "map -H/-C" to manual page

------------------------------------------------------------------------
r597 | lh3lh3 | 2008-04-22 23:19:43 +0100 (Tue, 22 Apr 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/read.h

 * maq-0.6.5-2
 * add <unistd.h> to mapcheck.cc
 * output multiple 01-mismatch hits

------------------------------------------------------------------------
r596 | lh3lh3 | 2008-04-22 21:57:19 +0100 (Tue, 22 Apr 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

trivial...

------------------------------------------------------------------------
r595 | lh3lh3 | 2008-04-22 13:10:32 +0100 (Tue, 22 Apr 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq_eval.pl-0.1.7
 * print out wrong SNPs for mono sites

------------------------------------------------------------------------
r593 | lh3lh3 | 2008-04-20 22:03:15 +0100 (Sun, 20 Apr 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/simulate.c

 * maq-0.6.5-1
 * spot a bug in simulate.c. not fixed, yet
 * non-SNPable regions are masked as lowcase letters

------------------------------------------------------------------------
r592 | lh3lh3 | 2008-04-20 22:01:49 +0100 (Sun, 20 Apr 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq_sanger.pl-0.1.12
 * allow to set maximum read length

------------------------------------------------------------------------
r590 | lh3lh3 | 2008-04-19 21:58:27 +0100 (Sat, 19 Apr 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq_sanger.pl-0.1.11
 * remove read name filtering
 * support alignment for reads in Solexa fastq format

------------------------------------------------------------------------
r589 | lh3lh3 | 2008-04-19 20:29:15 +0100 (Sat, 19 Apr 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq_sanger.pl-0.1.10
 * add gzip support
 * filtering read names (NOT use that!)

------------------------------------------------------------------------
r588 | lh3lh3 | 2008-04-19 20:25:54 +0100 (Sat, 19 Apr 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.11
 * support .gz files in cat2pair

------------------------------------------------------------------------
r587 | lh3lh3 | 2008-04-18 19:34:32 +0100 (Fri, 18 Apr 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

fix a bug

------------------------------------------------------------------------
r586 | lh3lh3 | 2008-04-12 00:01:50 +0100 (Sat, 12 Apr 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/asub

 * asub-0.1.3
 * add job dependency for SGE (have not tested yet)
 * add instructions

------------------------------------------------------------------------
r585 | lh3lh3 | 2008-04-12 00:01:04 +0100 (Sat, 12 Apr 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq_sanger.pl-0.1.8
 * change default parameters

------------------------------------------------------------------------
r581 | lh3lh3 | 2008-04-01 22:48:26 +0100 (Tue, 01 Apr 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/NEWS

clarifying some ambiguous point

------------------------------------------------------------------------
r580 | lh3lh3 | 2008-04-01 22:10:33 +0100 (Tue, 01 Apr 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl
   M /branches/lh3/maq/scripts/maq.pl

 * fq_all2std.pl-0.1.6
 * maq.pl-0.3.10
 * for convert the latest Illumina data

------------------------------------------------------------------------
r577 | lh3lh3 | 2008-03-28 23:26:11 +0000 (Fri, 28 Mar 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod

Release maq-0.6.5

------------------------------------------------------------------------
r576 | lh3lh3 | 2008-03-28 22:17:11 +0000 (Fri, 28 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/configure.ac

 * maq-0.6.4-9
 * assemble: fix a bug when reference is shorter than 3bp
 * update ChangeLog
 * prepare to release maq-0.6.5

------------------------------------------------------------------------
r575 | lh3lh3 | 2008-03-28 22:12:40 +0000 (Fri, 28 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/paf_utils.pl

 * paf_utils.pl-0.3.1
 * output normodds score if available

------------------------------------------------------------------------
r574 | lh3lh3 | 2008-03-27 13:02:07 +0000 (Thu, 27 Mar 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/csmap2ntmap.cc
   M /branches/lh3/maq/simulate.c

 * maq-0.6.4-8
 * fix a critical bug in csmap2nt
 * fix a potential memory violation in simulate. Thank Zamin Iqbal.

------------------------------------------------------------------------
r572 | lh3lh3 | 2008-03-26 23:06:33 +0000 (Wed, 26 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/csmap2ntmap.cc

 * maq-0.6.4-7
 * csmap2nt: remove the last color (this will not affect the result)
 * update ChangeLog
 * prepare to do the final test before release

------------------------------------------------------------------------
r570 | lh3lh3 | 2008-03-26 11:22:10 +0000 (Wed, 26 Mar 2008) | 8 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/rmdup.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.4-6
 * pair-dist is now the distance between 5'-end of the read. SOLiD distance
   will be affected.
 * the new distance may avoid potential inconsistency in previous version
 * for SOLiD, use PE mapping quality if there are 3 or fewer mismatches
 * in rmdup, avoid discarding some read pairs. However, it may still drop
   some read pairs with very short insert size.

------------------------------------------------------------------------
r569 | lh3lh3 | 2008-03-25 22:16:43 +0000 (Tue, 25 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_soa.cc

 * maq-0.6.4-5
 * fix a potential memory violation indelsoa

------------------------------------------------------------------------
r568 | lh3lh3 | 2008-03-25 15:28:11 +0000 (Tue, 25 Mar 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/csmap2ntmap.cc

 * maq-0.6.4-4
 * use dynamic programming to decode the nucleotide sequence. DP is more robust
   and consistent.

------------------------------------------------------------------------
r563 | lh3lh3 | 2008-03-25 13:08:06 +0000 (Tue, 25 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/csmap2ntmap.cc
   A /branches/lh3/maq-nt (from /branches/lh3/maq-xp:468)
   D /branches/lh3/maq-xp

 * maq (unfinished changes)
 * rename maq-xp as maq-nt

------------------------------------------------------------------------
r559 | lh3lh3 | 2008-03-24 22:06:29 +0000 (Mon, 24 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.9
 * add "-n" to SNPfilter

------------------------------------------------------------------------
r558 | lh3lh3 | 2008-03-24 21:59:50 +0000 (Mon, 24 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq_eval.pl-0.1.6
 * improve geno

------------------------------------------------------------------------
r557 | lh3lh3 | 2008-03-24 20:33:32 +0000 (Mon, 24 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.8
 * add a hidden parameter to SNPfilter

------------------------------------------------------------------------
r554 | lh3lh3 | 2008-03-23 21:02:23 +0000 (Sun, 23 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/configure.ac
   A /branches/lh3/maq/csmap2ntmap.cc
   M /branches/lh3/maq/indel_call.cc
   M /branches/lh3/maq/indel_soa.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/pileup.cc

 * maq-0.6.4-2
 * fix potential memory leak in assemble, pileup, indelpe, indelsoa, mapcheck
 * add csmap2nt, which converts cs .map file to nt .map file
   now SOLiD support has been accompished

------------------------------------------------------------------------
r553 | lh3lh3 | 2008-03-23 16:07:24 +0000 (Sun, 23 Mar 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/scripts/paf_utils.pl
   M /branches/lh3/maq/sort_mapping.cc

 * paf_utils.pl-0.3.0
 * add parser for shrimp
 * fix various bugs
 * maq-0.6.4-1
 * fix a bug related to long read names

------------------------------------------------------------------------
r549 | lh3lh3 | 2008-03-21 14:33:14 +0000 (Fri, 21 Mar 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/solid2fastq.pl
   A /branches/lh3/raf
   A /branches/lh3/raf/Makefile
   A /branches/lh3/raf/btree.c
   A /branches/lh3/raf/btree.h
   A /branches/lh3/raf/raf.c
   A /branches/lh3/raf/raf.h
   A /branches/lh3/raf/raf_index.c
   A /branches/lh3/raf/raf_index.h
   A /branches/lh3/raf/raf_main.c
   A /branches/lh3/raf/stdhash
   A /branches/lh3/raf/stdhash/stdhash.hh
   A /branches/lh3/raf/stdhash/stdhashc.cc
   A /branches/lh3/raf/stdhash/stdhashc.h
   A /branches/lh3/raf/zrlib
   A /branches/lh3/raf/zrlib/Makefile
   A /branches/lh3/raf/zrlib/adler32.c
   A /branches/lh3/raf/zrlib/compress.c
   A /branches/lh3/raf/zrlib/crc32.c
   A /branches/lh3/raf/zrlib/crc32.h
   A /branches/lh3/raf/zrlib/deflate.c
   A /branches/lh3/raf/zrlib/deflate.h
   A /branches/lh3/raf/zrlib/gzio.c
   A /branches/lh3/raf/zrlib/infback.c
   A /branches/lh3/raf/zrlib/inffast.c
   A /branches/lh3/raf/zrlib/inffast.h
   A /branches/lh3/raf/zrlib/inffixed.h
   A /branches/lh3/raf/zrlib/inflate.c
   A /branches/lh3/raf/zrlib/inflate.h
   A /branches/lh3/raf/zrlib/inftrees.c
   A /branches/lh3/raf/zrlib/inftrees.h
   A /branches/lh3/raf/zrlib/trees.c
   A /branches/lh3/raf/zrlib/trees.h
   A /branches/lh3/raf/zrlib/uncompr.c
   A /branches/lh3/raf/zrlib/zconf.h
   A /branches/lh3/raf/zrlib/zlib.h
   A /branches/lh3/raf/zrlib/zrio.c
   A /branches/lh3/raf/zrlib/zrio.h
   A /branches/lh3/raf/zrlib/zrio_main.c
   A /branches/lh3/raf/zrlib/zutil.c
   A /branches/lh3/raf/zrlib/zutil.h

This is Jue's maqindex, but C interface has been changed by me.

------------------------------------------------------------------------
r545 | lh3lh3 | 2008-03-16 19:57:55 +0000 (Sun, 16 Mar 2008) | 2 lines
Changed paths:
   A /branches/lh3/maq/scripts/solid2fastq.pl

convert SOLiD read format to fastq

------------------------------------------------------------------------
r536 | lh3lh3 | 2008-03-15 11:51:08 +0000 (Sat, 15 Mar 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac

Release maq-0.6.4

------------------------------------------------------------------------
r535 | lh3lh3 | 2008-03-15 11:03:40 +0000 (Sat, 15 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.7
 * fixed a bug in path recognization

------------------------------------------------------------------------
r534 | lh3lh3 | 2008-03-15 11:02:36 +0000 (Sat, 15 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq_sanger.pl-0.1.6
 * fix a bug

------------------------------------------------------------------------
r533 | lh3lh3 | 2008-03-14 23:26:02 +0000 (Fri, 14 Mar 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/paf_utils.pl

 * paf_utils.pl-0.2.1
 * improve the parser
 * add instructions

------------------------------------------------------------------------
r532 | lh3lh3 | 2008-03-14 21:38:01 +0000 (Fri, 14 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/paf_utils.pl

 * paf_utils.pl-0.2.0
 * convert .mapview file to .map

------------------------------------------------------------------------
r531 | lh3lh3 | 2008-03-14 12:52:21 +0000 (Fri, 14 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/subsnp.cc

 * maq-0.6.3-34
 * snpreg: also filter on the neighbouring quality

------------------------------------------------------------------------
r530 | lh3lh3 | 2008-03-14 10:36:28 +0000 (Fri, 14 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl

 * fq_all2std.pl-0.1.5
 * change for latest Illumina format

------------------------------------------------------------------------
r529 | lh3lh3 | 2008-03-13 23:54:17 +0000 (Thu, 13 Mar 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/scripts/maq.pl
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq.pl-0.3.6
 * change default -D in SNPfilter
 * maq_sanger.pl-0.1.5
 * skip directories
 * update documentations

------------------------------------------------------------------------
r528 | lh3lh3 | 2008-03-12 23:18:08 +0000 (Wed, 12 Mar 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

 * maq-0.6.3-33
 * Contradictary to my intuition, use 24bit in indexing is faster than 25bit
   indexing. Probably due to the cache efficiency (again)...

------------------------------------------------------------------------
r527 | lh3lh3 | 2008-03-12 21:26:59 +0000 (Wed, 12 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

 * maq-0.6.3-32
 * further improve cache efficiency a bit

------------------------------------------------------------------------
r526 | lh3lh3 | 2008-03-12 15:09:55 +0000 (Wed, 12 Mar 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/configure.ac

fix a bug in configure

------------------------------------------------------------------------
r525 | lh3lh3 | 2008-03-12 14:58:16 +0000 (Wed, 12 Mar 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc

 * maq-0.6.3-31
 * change macro _LONGSEED to _FASTMAP
 * in `fastmap' mode, seed_length=28, max_mismatch=3 and index_length=25
 * attempt to reduce the cache misses to the retrieval of seq->*
 * from this veersion, only seed length is at most 32bp

------------------------------------------------------------------------
r524 | lh3lh3 | 2008-03-11 23:57:58 +0000 (Tue, 11 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc

 * maq-0.6.3-30
 * further improve cache efficiency a bit

------------------------------------------------------------------------
r523 | lh3lh3 | 2008-03-11 19:37:50 +0000 (Tue, 11 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh

 * maq-0.6.3-29
 * add macro to use longer seed

------------------------------------------------------------------------
r522 | lh3lh3 | 2008-03-10 09:44:10 +0000 (Mon, 10 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/submap.c

 * maq-0.6.3-28
 * submap now acts as a filter for .map file

------------------------------------------------------------------------
r521 | lh3lh3 | 2008-03-07 11:07:48 +0000 (Fri, 07 Mar 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fastq2bfq.c
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-27
 * fix a bug in "maq map -N"
 * replace dw_shrink with a bit-shift function
 * a bit code clean up
 * attempt to improve the cache efficiency a bit (little effect though)

------------------------------------------------------------------------
r520 | lh3lh3 | 2008-03-07 08:53:22 +0000 (Fri, 07 Mar 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-26

------------------------------------------------------------------------
r519 | lh3lh3 | 2008-03-06 20:31:19 +0000 (Thu, 06 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/paf_utils.pl

 * paf_utils.pl-0.1.3
 * add parser for rmap

------------------------------------------------------------------------
r518 | lh3lh3 | 2008-03-06 20:30:36 +0000 (Thu, 06 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq_sanger.pl-0.1.4
 * fix a bug about the path of asub

------------------------------------------------------------------------
r517 | lh3lh3 | 2008-03-04 21:12:00 +0000 (Tue, 04 Mar 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc

 * maq-0.6.3-25
 * indel-pe apprarently works for SOLiD

------------------------------------------------------------------------
r516 | lh3lh3 | 2008-03-04 20:42:33 +0000 (Tue, 04 Mar 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-24
 * for SOLiD: "add pair afterward" now works
 * wait, I am going to add gapped alignment for SOLiD

------------------------------------------------------------------------
r515 | lh3lh3 | 2008-03-04 20:24:26 +0000 (Tue, 04 Mar 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/dword.hh
   M /branches/lh3/maq/match_aux.cc

 * maq-0.6.3-23
 * fix an ever existing bug. it is a typo actually...
 * wait, I will improve the part for SOLiD a bit later...

------------------------------------------------------------------------
r514 | lh3lh3 | 2008-03-04 16:02:25 +0000 (Tue, 04 Mar 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/scripts/maq_sanger.pl
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-22
 * fix a rare bug about minus insert size for ungapped alignment
 * fix a rare bug about extensive insert size for gapped alignment
 * maq_sanger.pl-0.1.4
 * add resource request by default

------------------------------------------------------------------------
r513 | lh3lh3 | 2008-03-03 15:36:15 +0000 (Mon, 03 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * fq_all2std.pl-0.1.4
 * export2xxx: change for the latest export format
 * maq_sanger.pl-0.1.3
 * add an example

------------------------------------------------------------------------
r512 | lh3lh3 | 2008-03-03 11:01:57 +0000 (Mon, 03 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/read.cc

 * maq-0.6.3-21
 * skip Smith-Waterman alignment if too few reads get mapped in pairs.
 * abort (instead of segfault) if all the reads are full of "N".
 * filtering polyA for single end reads now works

------------------------------------------------------------------------
r511 | lh3lh3 | 2008-03-03 10:57:16 +0000 (Mon, 03 Mar 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_sanger.pl

maq_sanger.pl now works with single end data from the Sanger Inst.

------------------------------------------------------------------------
r510 | lh3lh3 | 2008-03-02 10:51:57 +0000 (Sun, 02 Mar 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/scripts/maq_sanger.pl

 * maq-0.6.3-20
 * fix a stupid bug caused by the last modification
 * improve maq_sanger.pl

------------------------------------------------------------------------
r509 | lh3lh3 | 2008-03-01 23:02:25 +0000 (Sat, 01 Mar 2008) | 3 lines
Changed paths:
   A /branches/lh3/maq/scripts/asub
   A /branches/lh3/maq/scripts/maq_sanger.pl

 * asub: array-sub
 * maq_sanger.pl: do alignment in batch, for Sanger Inst's format ONLY

------------------------------------------------------------------------
r508 | lh3lh3 | 2008-03-01 22:33:01 +0000 (Sat, 01 Mar 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

a bug in SOLiD PE alignment

------------------------------------------------------------------------
r507 | lh3lh3 | 2008-03-01 17:10:28 +0000 (Sat, 01 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-18
 * assemble: change default -t to 0.93
 * map: for SOLiD reads, the correct orientation is:
   FF-read2-read1 or RR-read1-read2

------------------------------------------------------------------------
r506 | lh3lh3 | 2008-03-01 17:08:23 +0000 (Sat, 01 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl
   M /branches/lh3/maq/scripts/paf_utils.pl

 * paf_utils.pl-0.1.2
 * loose the criterion for a correct alignment (SOAP is troublesome)
 * maq.pl-0.3.5
 * filter on neighboring qualities

------------------------------------------------------------------------
r505 | lh3lh3 | 2008-03-01 00:09:05 +0000 (Sat, 01 Mar 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match_aux.cc

 * maq-0.6.3-17
 * mapstat: set the maximum mapQ as 99
 * update ChangeLog
 * fix a theoretical flaw in assemble. the accuracy affected little.

------------------------------------------------------------------------
r504 | lh3lh3 | 2008-02-29 13:31:26 +0000 (Fri, 29 Feb 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl
   M /branches/lh3/maq/scripts/paf_utils.pl

 * paf_utils.pl-0.1.1
 * print wrong alignment on demand
 * fq_all2std.pl-0.1.3
 * convert Bustard output (_prb.txt and _seq.txt) to fastq

------------------------------------------------------------------------
r503 | lh3lh3 | 2008-02-27 23:37:39 +0000 (Wed, 27 Feb 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/subsnp.cc

 * maq-0.6.3-16
 * calclate minimum neighbouring quality for each site
 * cns2snp/subpos are revised accordingly

------------------------------------------------------------------------
r502 | lh3lh3 | 2008-02-27 22:17:53 +0000 (Wed, 27 Feb 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/configure.ac

 * maq-0.6.3.-15
 * fix a theoretical error in `assemble'
 * the performance is quite close to the previous version

------------------------------------------------------------------------
r501 | lh3lh3 | 2008-02-25 14:42:28 +0000 (Mon, 25 Feb 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl
   D /branches/lh3/maq/scripts/parse_aln.pl

 * maq_eval.pl-0.1.5
 * add a less used hidden command for estimating FP. only for my own use.
 * parse_aln.pl has been renamed as saf_utils.pl

------------------------------------------------------------------------
r500 | lh3lh3 | 2008-02-25 11:39:29 +0000 (Mon, 25 Feb 2008) | 2 lines
Changed paths:
   A /branches/lh3/maq/scripts/paf_utils.pl (from /branches/lh3/maq/scripts/saf_utils.pl:499)
   D /branches/lh3/maq/scripts/saf_utils.pl

rename saf_utils.pl as paf_utils.pl

------------------------------------------------------------------------
r499 | lh3lh3 | 2008-02-25 11:38:57 +0000 (Mon, 25 Feb 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/saf_utils.pl

prepare to rename as paf_utils.pl

------------------------------------------------------------------------
r498 | lh3lh3 | 2008-02-25 11:22:07 +0000 (Mon, 25 Feb 2008) | 2 lines
Changed paths:
   D /branches/lh3/maq/scripts/gaf_utils.pl
   A /branches/lh3/maq/scripts/saf_utils.pl (from /branches/lh3/maq/scripts/gaf_utils.pl:497)

rename gaf_utils.pl to saf_utils.pl

------------------------------------------------------------------------
r497 | lh3lh3 | 2008-02-25 11:21:20 +0000 (Mon, 25 Feb 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/gaf_utils.pl

prepare to rename it as saf_utils.pl

------------------------------------------------------------------------
r496 | lh3lh3 | 2008-02-22 16:09:01 +0000 (Fri, 22 Feb 2008) | 2 lines
Changed paths:
   A /branches/lh3/maq/scripts/gaf_utils.pl (from /branches/lh3/maq/scripts/parse_aln.pl:495)

rename parse_aln.pl to gaf_utils.pl

------------------------------------------------------------------------
r495 | lh3lh3 | 2008-02-21 23:41:44 +0000 (Thu, 21 Feb 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/parse_aln.pl

 * uaf converter for maq
 * improve evaluation

------------------------------------------------------------------------
r494 | lh3lh3 | 2008-02-21 22:32:50 +0000 (Thu, 21 Feb 2008) | 3 lines
Changed paths:
   D /branches/lh3/maq/scripts/mapview.pl
   A /branches/lh3/maq/scripts/parse_aln.pl

 * convert parse_aln.pl to UAF alignment format
 * move mapview.pl to parse_aln.pl

------------------------------------------------------------------------
r493 | lh3lh3 | 2008-02-21 20:28:08 +0000 (Thu, 21 Feb 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/pileup.cc

 * maq-0.6.3-14
 * output base position on the read (for pileup)

------------------------------------------------------------------------
r492 | lh3lh3 | 2008-02-21 10:45:56 +0000 (Thu, 21 Feb 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/read.h
   M /branches/lh3/maq/scripts/maq.pl

 * maq-0.6.3-13
 * trim long adapter contaminations before alignment

------------------------------------------------------------------------
r491 | lh3lh3 | 2008-02-19 10:26:44 +0000 (Tue, 19 Feb 2008) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fasta2bfa.c
   M /branches/lh3/maq/simulate.c

 * maq-0.6.3-12
 * fix a bug in fasta2csfa: missing new line
 * more error output for simulate.c

------------------------------------------------------------------------
r490 | lh3lh3 | 2008-02-17 15:48:53 +0000 (Sun, 17 Feb 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/mapcheck.cc

 * maq-0.6.3-11
 * improve comments a bit
 * mapcheck: remove unused codes which never correctly worked
 * mapcheck: more stat

------------------------------------------------------------------------
r489 | lh3lh3 | 2008-02-17 14:33:25 +0000 (Sun, 17 Feb 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/scripts/maq.pl

 * maq-0.6.3-10
 * mapstat: output error rate
 * maq.pl-0.3.4
 * cat2pair: modified by "maq catfilter"

------------------------------------------------------------------------
r488 | lh3lh3 | 2008-02-16 19:29:21 +0000 (Sat, 16 Feb 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/read.cc

no change, actually

------------------------------------------------------------------------
r487 | lh3lh3 | 2008-02-16 19:10:49 +0000 (Sat, 16 Feb 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/read.cc

remove debug codes in read.cc

------------------------------------------------------------------------
r486 | lh3lh3 | 2008-02-16 19:07:42 +0000 (Sat, 16 Feb 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/read.cc

 * maq-0.6.3-9
 * filter for continous A. Only work for Sanger's PE cat format

------------------------------------------------------------------------
r485 | lh3lh3 | 2008-02-14 11:46:11 +0000 (Thu, 14 Feb 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/match_aux.cc

 * maq-0.6.3-8
 * update mapstat command

------------------------------------------------------------------------
r484 | lh3lh3 | 2008-02-13 16:02:19 +0000 (Wed, 13 Feb 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl

 * fq_all2std.pl-0.1.2
 * add support for SOLiD read format

------------------------------------------------------------------------
r483 | lh3lh3 | 2008-02-13 12:52:26 +0000 (Wed, 13 Feb 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/rmdup.cc
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.3
 * cat2pair: discriminate the two ends with "/1" and "/2"
 * improve fastq2bfq
 * maq-0.6.3-7
 * rmdup now records the number of checked pairs and removed pairs

------------------------------------------------------------------------
r482 | lh3lh3 | 2008-02-06 10:04:54 +0000 (Wed, 06 Feb 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maqmap.c

 * maq-0.6.3-6
 * fixed a neglectable bug in mapview

------------------------------------------------------------------------
r481 | lh3lh3 | 2008-02-04 22:21:27 +0000 (Mon, 04 Feb 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl

add /[12] when converting export format

------------------------------------------------------------------------
r480 | lh3lh3 | 2008-02-04 20:29:26 +0000 (Mon, 04 Feb 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/rmdup.cc
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-5
 * update ChangeLog
 * recognize "@read1/1" for the first read and "@read1/2" for the second
 * simulation/rmdup/map are all modified accordingly

------------------------------------------------------------------------
r479 | lh3lh3 | 2008-02-04 20:21:47 +0000 (Mon, 04 Feb 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_plot.pl

maq_plot.pl: make a bit better plot

------------------------------------------------------------------------
r478 | lh3lh3 | 2008-01-28 21:47:06 +0000 (Mon, 28 Jan 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc

 * maq-0.6.3-4
 * completely disable indelpe for SOLiD reads. It needs a lot of coding.

------------------------------------------------------------------------
r477 | lh3lh3 | 2008-01-28 21:29:38 +0000 (Mon, 28 Jan 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-3
 * store mismatch positions in .map file, at the cost of shorter read length
 * fix a bug in cns2win
 * mapview support for showing mismatch positions

------------------------------------------------------------------------
r473 | lh3lh3 | 2008-01-25 14:52:36 +0000 (Fri, 25 Jan 2008) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-2
 * change the meaning of "alternative mapping quality". Now it means: the
   lower SE mapping quality of the two ends (previously not)
 * have not tested, but I think I cannot be wrong... (hope I am right)

------------------------------------------------------------------------
r472 | lh3lh3 | 2008-01-23 20:00:55 +0000 (Wed, 23 Jan 2008) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.3-1
 * SOLiD PE reads are mapped as FF or RR, not FR

------------------------------------------------------------------------
r471 | lh3lh3 | 2008-01-23 11:02:20 +0000 (Wed, 23 Jan 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/mapview.pl

fix a minor error in reading the data

------------------------------------------------------------------------
r470 | lh3lh3 | 2008-01-18 20:00:23 +0000 (Fri, 18 Jan 2008) | 2 lines
Changed paths:
   A /branches/lh3/maq/scripts/mapview.pl

mapview.pl: parsing .map file with Perl

------------------------------------------------------------------------
r469 | lh3lh3 | 2008-01-18 10:12:35 +0000 (Fri, 18 Jan 2008) | 6 lines
Changed paths:
   M /branches/lh3/maq/scripts/farm-run.pl
   M /branches/lh3/maq/scripts/maq.pl

 * farm-run.pl-0.1.3
 * do not remove "/nfs" on the PATH
 * maq.pl-0.3.2
 * recognize relative path in easyrun
 * improve SNPfilter (thanks, Nathan)

------------------------------------------------------------------------
r465 | lh3lh3 | 2008-01-03 20:31:33 +0000 (Thu, 03 Jan 2008) | 2 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac

Release maq-0.6.3

------------------------------------------------------------------------
r463 | lh3lh3 | 2007-12-23 09:37:02 +0000 (Sun, 23 Dec 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/pileup.cc

 * maq-0.6.2-16
 * '-m' in "pileup" works. (fixed a bug)

------------------------------------------------------------------------
r462 | lh3lh3 | 2007-12-19 12:36:50 +0000 (Wed, 19 Dec 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/maq.pod

update documentations

------------------------------------------------------------------------
r461 | lh3lh3 | 2007-12-18 11:43:28 +0000 (Tue, 18 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fasta2bfa.c
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/subsnp.cc

 * maq-0.6.2-15
 * add "simucns" command to evaluate the consensus accuracy
 * add haploid support to "simulate"

------------------------------------------------------------------------
r460 | lh3lh3 | 2007-12-18 11:41:14 +0000 (Tue, 18 Dec 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.0
 * add haploid and single-end mode to "demo"

------------------------------------------------------------------------
r459 | lh3lh3 | 2007-12-18 03:24:47 +0000 (Tue, 18 Dec 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maqmap.c

 * maq-0.6.2-14
 * in mapview, output brief information (no sequences and qualities) 

------------------------------------------------------------------------
r458 | lh3lh3 | 2007-12-18 03:23:32 +0000 (Tue, 18 Dec 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.3.0
 * add codes to detect structural variations

------------------------------------------------------------------------
r457 | lh3lh3 | 2007-12-11 20:54:32 +0000 (Tue, 11 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/sort_mapping.cc

 * maq-0.6.2-13
 * take reads mapped with Smith-Waterman as paired
 * I am not sure whether this is the right to do, though.

------------------------------------------------------------------------
r456 | lh3lh3 | 2007-12-11 20:28:42 +0000 (Tue, 11 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/pair_stat.cc
   M /branches/lh3/maq/scripts/maq_plot.pl

 * maq-0.6.2-12
 * show abnormal pairs
 * plotting abnormal pairs works again

------------------------------------------------------------------------
r455 | lh3lh3 | 2007-12-10 11:51:08 +0000 (Mon, 10 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/rmdup.cc

 * maq-0.6.2-11
 * a typo in previous check in
 * still name it as 0.6.2-11

------------------------------------------------------------------------
r454 | lh3lh3 | 2007-12-10 11:48:56 +0000 (Mon, 10 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/rmdup.cc

 * maq-0.6.2-11
 * avoid potential missing hits (a minor bug)
 * rmdup now recognizes "-"

------------------------------------------------------------------------
r453 | lh3lh3 | 2007-12-10 11:26:49 +0000 (Mon, 10 Dec 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

 * maq-0.6.2-10
 * increase the randomness of the seed

------------------------------------------------------------------------
r452 | lh3lh3 | 2007-12-09 12:05:15 +0000 (Sun, 09 Dec 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

 * 0.6.2-9
 * change back to random seed, which actually is more robust

------------------------------------------------------------------------
r450 | lh3lh3 | 2007-12-06 21:47:19 +0000 (Thu, 06 Dec 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq.pl-0.2.0
 * easyrun now works PE reads
 * add 'demo' for simulation+easyrun+maq_eval
 * maq_eval.pl-0.1.4
 * increase robustness

------------------------------------------------------------------------
r443 | lh3lh3 | 2007-12-06 15:32:05 +0000 (Thu, 06 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/pair_stat.cc

 * maq-0.6.2-8
 * in map, change back to the previous way to score a hit
 * in paircov, add "count non-N region" and remove some useless codes

------------------------------------------------------------------------
r442 | lh3lh3 | 2007-12-05 14:26:22 +0000 (Wed, 05 Dec 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/pair_stat.cc
   M /branches/lh3/maq/subsnp.cc

 * maq-0.6.2-7
 * LaDeana Hillier finally persuaded me that mismatches should be counted
   in scoring a hit. I do that now.
 * `paircov' now works again, which also finds absolute break points
 * `snpreg' now moves to subsnp.cc. It can also filter SNPs now.

------------------------------------------------------------------------
r441 | lh3lh3 | 2007-12-03 11:48:43 +0000 (Mon, 03 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

 * maq-0.6.2-6
 * snpreg: output SNP-callable regions given different quality threshold
 * map: use fixed seed to random numbers

------------------------------------------------------------------------
r440 | lh3lh3 | 2007-12-03 11:46:58 +0000 (Mon, 03 Dec 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq_eval.pl-0.1.3
 * in indelsoa, filter SNPs
 * in indelpe, output FN and FP

------------------------------------------------------------------------
r439 | lh3lh3 | 2007-12-01 16:14:38 +0000 (Sat, 01 Dec 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq_eval.pl-0.1.2
 * evaluate genotyping sites

------------------------------------------------------------------------
r438 | lh3lh3 | 2007-11-30 12:34:24 +0000 (Fri, 30 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.10
 * change the option names in SNPfilter

------------------------------------------------------------------------
r437 | lh3lh3 | 2007-11-29 15:10:28 +0000 (Thu, 29 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h

 * maq-0.6.2-5
 * add "snpreg" command: calculate regions where SNP can be called

------------------------------------------------------------------------
r436 | lh3lh3 | 2007-11-26 13:09:15 +0000 (Mon, 26 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.9
 * in easyrun, fix a typo caused by the last revision

------------------------------------------------------------------------
r435 | lh3lh3 | 2007-11-26 09:53:29 +0000 (Mon, 26 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fastq2bfq.c

 * maq-0.6.2-4
 * in fastq2bfq, avoid generating empty files

------------------------------------------------------------------------
r434 | lh3lh3 | 2007-11-26 09:52:22 +0000 (Mon, 26 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.8
 * in easyrun, split the input fastq to smaller files if necessary

------------------------------------------------------------------------
r433 | lh3lh3 | 2007-11-25 23:19:38 +0000 (Sun, 25 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/simulate.c

 * maq-0.6.3
 * fix a stupid bug in simulation

------------------------------------------------------------------------
r432 | lh3lh3 | 2007-11-25 23:01:03 +0000 (Sun, 25 Nov 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/simulate.c

 * maq-0.6.2-2
 * make coordinate more accurate, but cannot be absolutely accurate
 * improve simustat to tolerate indel alignment 

------------------------------------------------------------------------
r430 | lh3lh3 | 2007-11-25 21:07:18 +0000 (Sun, 25 Nov 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/simulate.c

 * maq-0.6.2-1
 * simulate reads for diploid reference
 * known bug: the coordinate of some reads is wrong.

------------------------------------------------------------------------
r427 | lh3lh3 | 2007-11-23 22:19:15 +0000 (Fri, 23 Nov 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod

Release maq-0.6.2

------------------------------------------------------------------------
r426 | lh3lh3 | 2007-11-23 17:17:47 +0000 (Fri, 23 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/eland2maq.cc

 * maq-0.6.1-18
 * export2maq: fix a bug in converting base qualities

------------------------------------------------------------------------
r425 | lh3lh3 | 2007-11-23 16:03:21 +0000 (Fri, 23 Nov 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/eland2maq.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h

 * maq-0.6.1-17
 * convert Solexa's export format to maq's .map format
 * add NEWS and prepare to release maq-0.6.2

------------------------------------------------------------------------
r424 | lh3lh3 | 2007-11-19 16:30:56 +0000 (Mon, 19 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/mapcheck.cc

 * maq-0.6.1-15
 * fix a compiling error for some powerpc64-linux

------------------------------------------------------------------------
r422 | lh3lh3 | 2007-11-19 09:33:41 +0000 (Mon, 19 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/fq_all2std.pl

 * fq_all2std.pl-0.1.1
 * fix a bug for "export" format

------------------------------------------------------------------------
r420 | lh3lh3 | 2007-11-18 23:16:49 +0000 (Sun, 18 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.1
 * for Solexa's new export format

------------------------------------------------------------------------
r419 | lh3lh3 | 2007-11-18 23:16:02 +0000 (Sun, 18 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/farm-run.pl

 * farm-run.pl-0.12
 * correct uname for a Linux machine

------------------------------------------------------------------------
r418 | lh3lh3 | 2007-11-16 10:19:35 +0000 (Fri, 16 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.6
 * fastq2bfq: for Solexa's new "export" format

------------------------------------------------------------------------
r417 | lh3lh3 | 2007-11-16 10:11:59 +0000 (Fri, 16 Nov 2007) | 3 lines
Changed paths:
   A /branches/lh3/maq/scripts/fq_all2std.pl

 * fq_all2std.pl-0.1.0
 * script for converting between various formats

------------------------------------------------------------------------
r414 | lh3lh3 | 2007-11-15 10:01:48 +0000 (Thu, 15 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

 * maq-0.6.1-15
 * fix a bug related to max_err10

------------------------------------------------------------------------
r411 | lh3lh3 | 2007-11-08 15:48:01 +0000 (Thu, 08 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/pileup.cc

 * 0.6.1-14
 * allow to use "-" in many more commands

------------------------------------------------------------------------
r410 | lh3lh3 | 2007-11-08 10:40:14 +0000 (Thu, 08 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/configure.ac

 * 0.6.1-13
 * allow to use "-" in "assemble"

------------------------------------------------------------------------
r401 | lh3lh3 | 2007-11-01 15:50:37 +0000 (Thu, 01 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.5
 * sorry, fix another bug

------------------------------------------------------------------------
r400 | lh3lh3 | 2007-11-01 15:20:52 +0000 (Thu, 01 Nov 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc

 * maq-0.6.1-12
 * fix a bug in indelpe (caused by previous debugging codes)

------------------------------------------------------------------------
r399 | lh3lh3 | 2007-11-01 15:20:00 +0000 (Thu, 01 Nov 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.4
 * fix a bug in fastq2bfq
 * improve cat2pair

------------------------------------------------------------------------
r395 | lh3lh3 | 2007-10-31 15:22:40 +0000 (Wed, 31 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.3
 * improve fastq2bfq powered by the new 'maq fastq2bfq'

------------------------------------------------------------------------
r394 | lh3lh3 | 2007-10-31 11:59:10 +0000 (Wed, 31 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fastq2bfq.c

 * 0.6.1-11
 * improve fastq2bfq command

------------------------------------------------------------------------
r393 | lh3lh3 | 2007-10-31 11:13:12 +0000 (Wed, 31 Oct 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc

 * maq-0.6.1-10
 * allow to change max_err10 on the command-line
 * set the minimum length of reads to 16bp, instead of 20bp

------------------------------------------------------------------------
r392 | lh3lh3 | 2007-10-31 11:10:57 +0000 (Wed, 31 Oct 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.2
 * allow to set the maximum read depth in SNPfilter
 * improve fastq2bfq a bit

------------------------------------------------------------------------
r384 | lh3lh3 | 2007-10-30 09:35:43 +0000 (Tue, 30 Oct 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/maq.pod

 * 0.6.1-9
 * update documentations
 * fix a bug in indelpe

------------------------------------------------------------------------
r379 | lh3lh3 | 2007-10-29 09:23:46 +0000 (Mon, 29 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

 * maq_eval.pl-0.1.1
 * better evaluation for indelsoa

------------------------------------------------------------------------
r378 | lh3lh3 | 2007-10-28 21:59:46 +0000 (Sun, 28 Oct 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/maq.pod

explain SNPfilter and indelsoa

------------------------------------------------------------------------
r377 | lh3lh3 | 2007-10-28 20:59:40 +0000 (Sun, 28 Oct 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_soa.cc
   M /branches/lh3/maq/main.c

 * maq-0.6.1-8
 * make indelsoa public
 * indelsoa should be able to work with multiple references (not tested)
 * output an alternative score in indelsoa
 * change a threshold in aux_utils.c

------------------------------------------------------------------------
r376 | lh3lh3 | 2007-10-28 20:53:07 +0000 (Sun, 28 Oct 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.1
 * change the SNPfilter for indelsoa (left+right-across>=3 && across<=1)
 * in easyrun, indelsoa-filtered SNPs become the default.

------------------------------------------------------------------------
r375 | lh3lh3 | 2007-10-28 18:32:51 +0000 (Sun, 28 Oct 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

 * maq.pl-0.1.0
 * improve `SNPfilter' command
 * improve `gwhich()'
 * improve `easyrun' command
 * add `statmap' command (previously known as `stat_err.pl'))

------------------------------------------------------------------------
r374 | lh3lh3 | 2007-10-28 15:54:01 +0000 (Sun, 28 Oct 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq_eval.pl

put indel evaluation in the script

------------------------------------------------------------------------
r373 | lh3lh3 | 2007-10-26 22:25:20 +0100 (Fri, 26 Oct 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/eland2maq.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/maq.pod

 * 0.6.1-7
 * change the default quality to 25
 * update the documentation

------------------------------------------------------------------------
r372 | lh3lh3 | 2007-10-26 22:23:08 +0100 (Fri, 26 Oct 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

change the SNP filter

------------------------------------------------------------------------
r371 | lh3lh3 | 2007-10-26 14:29:54 +0100 (Fri, 26 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.6.1-6
 * dump unmapped reads to a separate file

------------------------------------------------------------------------
r370 | lh3lh3 | 2007-10-26 12:51:09 +0100 (Fri, 26 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.6.1-5
 * dump unmapped reads and poorly mapped reads

------------------------------------------------------------------------
r369 | lh3lh3 | 2007-10-26 11:12:12 +0100 (Fri, 26 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/pileup.cc

 * 0.6.1-4
 * bring back 'assemble/pileup -m' to meet users' request

------------------------------------------------------------------------
r361 | lh3lh3 | 2007-10-13 22:13:01 +0100 (Sat, 13 Oct 2007) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/eland2maq.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/read.cc

 * 0.6.1-3
 * fix the bug in methy_mode
 * eland2maq now works properly
 * allow G->A alignment in methy_mode

------------------------------------------------------------------------
r360 | lh3lh3 | 2007-10-13 14:22:57 +0100 (Sat, 13 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   A /branches/lh3/maq/eland2maq.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/maqmap.h

 * 0.6.1-2
 * add eland2maq: convert eland output to maq alignment

------------------------------------------------------------------------
r347 | lh3lh3 | 2007-10-10 16:01:58 +0100 (Wed, 10 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

 * 0.6.1-1
 * fix a bug in methylation alignment

------------------------------------------------------------------------
r332 | lh3lh3 | 2007-10-03 20:55:06 +0100 (Wed, 03 Oct 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/FUTURES
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac

Release maq-0.6.1

------------------------------------------------------------------------
r328 | lh3lh3 | 2007-10-02 13:38:41 +0100 (Tue, 02 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/read.cc

 * 0.6.0-6
 * fix a bug for methy-mode. I know few are using this, but it is a bug anyway.

------------------------------------------------------------------------
r327 | lh3lh3 | 2007-10-02 13:05:22 +0100 (Tue, 02 Oct 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c

 * 0.6.0-5
 * fix a rare bug in get_pos.c

------------------------------------------------------------------------
r315 | lh3lh3 | 2007-09-26 11:14:17 +0100 (Wed, 26 Sep 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/read.h
   M /branches/lh3/maq/sort_mapping.cc

 * 0.6.0-4
 * make trim-adapter work properly

------------------------------------------------------------------------
r284 | lh3lh3 | 2007-09-19 15:13:42 +0100 (Wed, 19 Sep 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fastq2bfq.c

 * 0.6.0-3
 * 0.6.0-2 is prematured.
 * change zero quality to 1 (in fastq2bfq)

------------------------------------------------------------------------
r251 | lh3lh3 | 2007-09-10 13:43:36 +0100 (Mon, 10 Sep 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.6.0-1
 * map a read to the position that gives the minimum sum of quality values
   of mismatched bases. Previously maq first compares the number of mismatches
   in the first 24bp and then check the sum.
 * on simulated data, this gives slightly better accuracy.

------------------------------------------------------------------------
r248 | lh3lh3 | 2007-09-05 13:11:06 +0100 (Wed, 05 Sep 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/FUTURES
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod

Release 0.6.0

------------------------------------------------------------------------
r247 | lh3lh3 | 2007-09-05 10:24:26 +0100 (Wed, 05 Sep 2007) | 7 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/rmdup.cc

 * 0.5.1-24
 * output number of 0- and 1-mismatch hits in mapview
 * when '-p' is flagged with assemble, abnormal pairs will be discarded, instead
   of being assigned a quality zero
 * fix a bug in rmdup which may causes segmentation fault in rare cases
 * add more documentations

------------------------------------------------------------------------
r244 | lh3lh3 | 2007-08-29 17:07:08 +0100 (Wed, 29 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-23
 * revert some codes from 0.5.1-6

------------------------------------------------------------------------
r243 | lh3lh3 | 2007-08-29 16:43:52 +0100 (Wed, 29 Aug 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-22
 * remove debugging codes from simulate.c
 * fix two trivial/potential bugs in sort_mapping.c 

------------------------------------------------------------------------
r242 | lh3lh3 | 2007-08-29 10:53:29 +0100 (Wed, 29 Aug 2007) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/simulate.c

 * 0.5.1-21
 * fix a bug in calculating the average insert size (caused by latest modifications)
 * simulate now generates reads on both strand (previously read1 from forward,
   and read2 always from reverse strand)

------------------------------------------------------------------------
r241 | lh3lh3 | 2007-08-28 13:49:52 +0100 (Tue, 28 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/simulate.c

 * 0.5.1-20
 * fix problems caused by previous revision

------------------------------------------------------------------------
r240 | lh3lh3 | 2007-08-28 10:53:18 +0100 (Tue, 28 Aug 2007) | 7 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/maqmap.h
   A /branches/lh3/maq/rmdup.cc
   D /branches/lh3/maq/rmpair.cc
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-19
 * in maqmap1_t, dist now shows the insert size.
 * rmdup is rewritten. it now handles abnormal pairs.
 * after Smith-Waterman, reads without indels will also be saved, though not used at later step
 * simulate is able to generate different read lengths from the length in the fqc_t
 * this revision has not been thoroughly tested.

------------------------------------------------------------------------
r238 | lh3lh3 | 2007-08-23 10:21:48 +0100 (Thu, 23 Aug 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/maq.pod

for changes after 0.5.1

------------------------------------------------------------------------
r235 | lh3lh3 | 2007-08-22 09:09:04 +0100 (Wed, 22 Aug 2007) | 7 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/rmpair.cc
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-18
 * output version number in 'map'
 * detect duplicated read names in 'rmdup'
 * in attempt to use another filter
 * initiate Smith-Waterman alignment for Q20 reads (not Q30)
 * generate unique read names in 'simulate'

------------------------------------------------------------------------
r234 | lh3lh3 | 2007-08-20 09:49:23 +0100 (Mon, 20 Aug 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/merge.cc

 * 0.5.1-17
 * mapmerge: allow to dump .map to stdout
 * indel_pe: check boundaries before alignment

------------------------------------------------------------------------
r233 | lh3lh3 | 2007-08-13 20:36:50 +0100 (Mon, 13 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/read.cc

 * 0.5.1-16
 * fix a bug in adapter trimming

------------------------------------------------------------------------
r232 | lh3lh3 | 2007-08-10 23:05:48 +0100 (Fri, 10 Aug 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.c
   A /branches/lh3/maq/indel_call.cc

 * 0.5.1-15
 * indelpe: indel calling from PE reads
 * better combine indelsoa and indelpe to give better results (future plan)

------------------------------------------------------------------------
r231 | lh3lh3 | 2007-08-10 21:27:32 +0100 (Fri, 10 Aug 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.h
   A /branches/lh3/maq/get_pos.c (from /branches/lh3/maq/get_pos.cc:230)
   D /branches/lh3/maq/get_pos.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h

rename get_pos.cc->get_pos.c

------------------------------------------------------------------------
r230 | lh3lh3 | 2007-08-10 20:27:35 +0100 (Fri, 10 Aug 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/bfa.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.cc
   M /branches/lh3/maq/indel_pe.cc

 * 0.5.1-14
 * fix a minor bug in indel_pe.cc
 * prepare to rename get_pos.cc

------------------------------------------------------------------------
r229 | lh3lh3 | 2007-08-10 14:02:35 +0100 (Fri, 10 Aug 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.cc
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-13
 * indel_pe seems to work properly
 * need to write someting to pull out all the indel sites

------------------------------------------------------------------------
r228 | lh3lh3 | 2007-08-09 23:27:47 +0100 (Thu, 09 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1.-12
 * the core part of indelpe works. more work need to be done, though

------------------------------------------------------------------------
r227 | lh3lh3 | 2007-08-09 14:30:38 +0100 (Thu, 09 Aug 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/maqmap.h
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/rmpair.cc
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-11
 * in methylation alignment mode, change all C to T. this is the only right way.
 * a little change in calculating mapping qualities. should not matter much for high-quality reads
 * write more codes for the indel detector
 * this revision probably cannot work!

------------------------------------------------------------------------
r226 | lh3lh3 | 2007-08-08 16:41:24 +0100 (Wed, 08 Aug 2007) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   A /branches/lh3/maq/indel_pe.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/rmpair.cc
   M /branches/lh3/maq/scripts/maq.pl
   M /branches/lh3/maq/sort_mapping.cc
   A /branches/lh3/maq/stdaln.c
   A /branches/lh3/maq/stdaln.h

 * 0.5.1-10
 * rmdup: fix a bug
 * easyrun: allow to filter adapter at the command-line
 * prepare to add indel detector for PE reads. just started.

------------------------------------------------------------------------
r225 | lh3lh3 | 2007-08-07 16:09:30 +0100 (Tue, 07 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/read.h

 * 0.5.1-9
 * more sophisticated 3'-adapter trimmer

------------------------------------------------------------------------
r224 | lh3lh3 | 2007-08-06 23:29:29 +0100 (Mon, 06 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/read.h

 * 0.5.1-8
 * alignment for methylated data

------------------------------------------------------------------------
r223 | lh3lh3 | 2007-08-06 00:20:36 +0100 (Mon, 06 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/read.cc

 * 0.5.1-7
 * fix bug in auto_trim(), but this does not work well...

------------------------------------------------------------------------
r222 | lh3lh3 | 2007-08-05 17:11:23 +0100 (Sun, 05 Aug 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc

0.5.1-6: trivial changes

------------------------------------------------------------------------
r221 | lh3lh3 | 2007-08-04 22:57:40 +0100 (Sat, 04 Aug 2007) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.cc
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/maqmap.h
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/pileup.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-5
 * discard reads that give large sum of errors. For real data, this helps A LOT!
 * maqstat is now disfunctional...
 * allow to adjust MAF in assemble

------------------------------------------------------------------------
r220 | lh3lh3 | 2007-08-04 16:30:12 +0100 (Sat, 04 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-4
 * fix a bug caused by the operator precedence

------------------------------------------------------------------------
r218 | lh3lh3 | 2007-08-04 14:53:43 +0100 (Sat, 04 Aug 2007) | 7 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-3
 * reduce unnecessary memory usage (a bit)
 * fix a subtle and minor bug in calculating paired end mapping qualities
 * hash word in a more efficient way, especially for long reads
 * now the mapping quality seems to be underestimated...
 * at least on bacteria, the new code is giving better alignments

------------------------------------------------------------------------
r217 | lh3lh3 | 2007-08-04 00:38:41 +0100 (Sat, 04 Aug 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/rmpair.cc
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.1-2
 * simulate.c: fixed a bug for the reverse read
 * simulate.c: added forgotten gzclose()
 * align long but low-quality reads
 * mapping quality is overestimated a bit

------------------------------------------------------------------------
r216 | lh3lh3 | 2007-08-03 22:50:40 +0100 (Fri, 03 Aug 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/rmpair.cc

 * 0.5.1-1
 * fix a minor bug in rmpair.cc

------------------------------------------------------------------------
r212 | lh3lh3 | 2007-07-31 11:19:16 +0100 (Tue, 31 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/FUTURES
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/match.cc

Release 0.5.1

------------------------------------------------------------------------
r211 | lh3lh3 | 2007-07-31 09:12:07 +0100 (Tue, 31 Jul 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/maq.pod
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/rmpair.cc

 * 0.5.0-14 (the following also shows changes in 0.5.0-13)
 * change the way the final mapping quality is determined in "assemble"
 * output clean up
 * better POD
 * prepare to release 0.5.1

------------------------------------------------------------------------
r210 | lh3lh3 | 2007-07-30 17:18:49 +0100 (Mon, 30 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.cc
   M /branches/lh3/maq/maq.pod

 * 0.5.0-13
 * later... I am catching bus...

------------------------------------------------------------------------
r209 | lh3lh3 | 2007-07-30 10:31:57 +0100 (Mon, 30 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/maq.pod

better documentations

------------------------------------------------------------------------
r207 | lh3lh3 | 2007-07-29 23:32:33 +0100 (Sun, 29 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/main.c
   A /branches/lh3/maq/maq.pod

add POD manual

------------------------------------------------------------------------
r206 | lh3lh3 | 2007-07-29 16:19:38 +0100 (Sun, 29 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/scripts/maq.pl
   M /branches/lh3/maq/simulate.c

 * 0.5.0-12
 * dump fastq statistics into a separate data file.

------------------------------------------------------------------------
r205 | lh3lh3 | 2007-07-27 13:39:10 +0100 (Fri, 27 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/read.cc
   M /branches/lh3/maq/read.h
   M /branches/lh3/maq/scripts/maq.pl

 * 0.5.0-11
 * automatically trim all reads (not the default option)

------------------------------------------------------------------------
r204 | lh3lh3 | 2007-07-27 08:47:59 +0100 (Fri, 27 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fasta2bfa.c

 * 0.5.0-10
 * fix bug in fakemut

------------------------------------------------------------------------
r202 | lh3lh3 | 2007-07-26 10:27:52 +0100 (Thu, 26 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/simulate.c

 * 0.5.0-9
 * fix a bug in "map".

------------------------------------------------------------------------
r201 | lh3lh3 | 2007-07-25 12:54:43 +0100 (Wed, 25 Jul 2007) | 7 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/simulate.c
   M /branches/lh3/maq/sort_mapping.cc

 * 0.5.0-8
 * match.cc: fix a bug which will cause tandem repetitive pairs lost
 * change the default minimum insert size to 0
 * sort_mapping.cc: fix a bug in calculating paired mapping qualities. However,
   decide to make it more conservative at last.
 * simulate.c: add codes to evaluate mappings based on simulated reads

------------------------------------------------------------------------
r199 | lh3lh3 | 2007-07-23 17:17:55 +0100 (Mon, 23 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match_aux.cc

 * 0.5.0-7
 * improve help
 * change default paired end distance to [60,250]

------------------------------------------------------------------------
r198 | lh3lh3 | 2007-07-23 16:45:49 +0100 (Mon, 23 Jul 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/configure.ac
   A /branches/lh3/maq/genran.c
   A /branches/lh3/maq/genran.h
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   A /branches/lh3/maq/rmpair.cc
   M /branches/lh3/maq/scripts/maq_eval.pl
   M /branches/lh3/maq/simulate.c
   A /branches/lh3/maq/submap.c

 * 0.5.0-6
 * It seems that I forgot to add files at the last check-in
 * add rmpair.cc: remove pairs with the exact coordinates
 * add submap.c: extract a submap. Note that the resultant file is slightly different in teh format.
 * finish simulate.c: simulate paired reads

------------------------------------------------------------------------
r188 | lh3lh3 | 2007-07-19 12:29:51 +0100 (Thu, 19 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/subsnp.cc

 * 0.5.0-4
 * distinguish het1 and het2

------------------------------------------------------------------------
r187 | lh3lh3 | 2007-07-19 00:39:08 +0100 (Thu, 19 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/assopt.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/pileup.cc
   M /branches/lh3/maq/stdhash.hh

 * 0.5.0-3
 * add a few trivial things. little improvement, though

------------------------------------------------------------------------
r185 | lh3lh3 | 2007-07-18 11:20:51 +0100 (Wed, 18 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/maqmap.c

 * 0.5.0-2
 * write D codes as C/C++ codes
 * have not test it yet

------------------------------------------------------------------------
r183 | lh3lh3 | 2007-07-18 00:05:47 +0100 (Wed, 18 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/match_aux.cc

 * 0.5.0-1
 * avoid using maqmap_t::n_mapped_reads

------------------------------------------------------------------------
r170 | lh3lh3 | 2007-07-14 17:45:40 +0100 (Sat, 14 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/NEWS

change to r171

------------------------------------------------------------------------
r169 | lh3lh3 | 2007-07-14 17:44:42 +0100 (Sat, 14 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/ChangeLog
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/NEWS
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c

MAQ Release 0.5.0

------------------------------------------------------------------------
r167 | lh3lh3 | 2007-07-13 15:02:44 +0100 (Fri, 13 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/altchr.cc
   M /branches/lh3/maq/configure.ac

 * fix a bug in altchr.cc
 * 0.4.3-13

------------------------------------------------------------------------
r166 | lh3lh3 | 2007-07-13 10:09:00 +0100 (Fri, 13 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   A /branches/lh3/maq/altchr.cc
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/const.c
   M /branches/lh3/maq/const.h
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h

 * 0.4.3-12
 * add altchr.cc

------------------------------------------------------------------------
r165 | lh3lh3 | 2007-07-12 15:30:32 +0100 (Thu, 12 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/maq/scripts/maq.pl

allow to trim reads on the command line.

------------------------------------------------------------------------
r164 | lh3lh3 | 2007-07-12 14:47:20 +0100 (Thu, 12 Jul 2007) | 6 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/maqmap_conv.c
   D /branches/lh3/maq/scripts/eval_snp.pl
   M /branches/lh3/maq/scripts/maq.pl
   A /branches/lh3/maq/scripts/maq_eval.pl (from /branches/lh3/maq/scripts/eval_snp.pl:160)
   M /branches/lh3/maq/scripts/maq_plot.pl

 * 0.4.3-11
 * format check in maqmap.c and maqmap_conv.c
 * rename eval_snp.pl as maq_eval.pl
 * allow to change xtics in maq_plot.pl
 * improve maq.pl

------------------------------------------------------------------------
r163 | lh3lh3 | 2007-07-11 23:23:15 +0100 (Wed, 11 Jul 2007) | 7 lines
Changed paths:
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/maqmap.c
   M /branches/lh3/maq/maqmap.h
   M /branches/lh3/maq/maqmap_conv.c
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/merge.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.4.3-10
 * move mapview to maqmap.c. it is a good example
 * fix a bug in mapmerge, which is caused by the new maqmap interface
 * run valgrind on a couple of commands: map, mapmerge, indelsoa, assemble,
   pileup, mapcheck, mapview and mapass2maq
	   

------------------------------------------------------------------------
r162 | lh3lh3 | 2007-07-11 22:27:31 +0100 (Wed, 11 Jul 2007) | 5 lines
Changed paths:
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/assemble.h
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/get_pos.cc
   M /branches/lh3/maq/indel_soa.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/main.h
   M /branches/lh3/maq/mapcheck.cc
   A /branches/lh3/maq/maqmap.c
   A /branches/lh3/maq/maqmap.h
   A /branches/lh3/maq/maqmap_conv.c
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match.hh
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/merge.cc
   M /branches/lh3/maq/pair_stat.cc
   M /branches/lh3/maq/pileup.cc
   M /branches/lh3/maq/sort_mapping.cc

 * 0.4.3-9
 * new interface to .map format. read names will be stored.
 * match seemingly generates correct result
 * other functions need thorough testing

------------------------------------------------------------------------
r161 | lh3lh3 | 2007-07-11 13:43:49 +0100 (Wed, 11 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/maq/INSTALL
   M /branches/lh3/maq/Makefile.am
   M /branches/lh3/maq/Makefile.generic
   M /branches/lh3/maq/README
   M /branches/lh3/maq/assemble.cc
   M /branches/lh3/maq/aux_utils.c
   M /branches/lh3/maq/configure.ac
   M /branches/lh3/maq/fasta2bfa.c
   M /branches/lh3/maq/fastq2bfq.c
   M /branches/lh3/maq/indel_soa.cc
   M /branches/lh3/maq/main.c
   M /branches/lh3/maq/mapcheck.cc
   M /branches/lh3/maq/match.cc
   M /branches/lh3/maq/match_aux.cc
   M /branches/lh3/maq/merge.cc
   M /branches/lh3/maq/pair_stat.cc
   M /branches/lh3/maq/pileup.cc
   M /branches/lh3/maq/rbcc.cc
   M /branches/lh3/maq/read.cc
   D /branches/lh3/maq/scripts/mapass2.pl
   D /branches/lh3/maq/scripts/mapass2_plot.pl
   A /branches/lh3/maq/scripts/maq.pl (from /branches/lh3/maq/scripts/mapass2.pl:160)
   A /branches/lh3/maq/scripts/maq_plot.pl (from /branches/lh3/maq/scripts/mapass2_plot.pl:160)
   M /branches/lh3/maq/subsnp.cc

 * rename mapass2 as maq
 * 0.4.3-8

------------------------------------------------------------------------
r159 | lh3lh3 | 2007-07-11 13:26:43 +0100 (Wed, 11 Jul 2007) | 9 lines
Changed paths:
   A /branches/lh3/maq (from /branches/lh3/mapass2:158)

Mapass2 is renamed as "maq", which stands for Mapping and
Assembly with Qualities. It is pronounced in the same way
as "Mac", the Apple's operating system.

The mapass2 will be stopped and all the new development will
happen in /branches/lh3/maq. The current version of mapass2 at
this branching point is: 0.4.3-7. Today is 11 July 2007.


------------------------------------------------------------------------
r158 | lh3lh3 | 2007-07-10 21:39:12 +0100 (Tue, 10 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/indel_soa.cc
   M /branches/lh3/mapass2/scripts/mapass2.pl

 * 0.4.3-7
 * improve indel detection (only works for homozygous indels!)
 * mapass2.pl: filter out SNPs falling in indels regions

------------------------------------------------------------------------
r157 | lh3lh3 | 2007-07-10 19:34:22 +0100 (Tue, 10 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile.am
   M /branches/lh3/mapass2/Makefile.generic
   M /branches/lh3/mapass2/configure.ac
   A /branches/lh3/mapass2/indel_soa.cc
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/pair_stat.cc

 * 0.4.3-5
 * state-of-art indel detector (will be improved later)

------------------------------------------------------------------------
r156 | lh3lh3 | 2007-07-09 23:53:07 +0100 (Mon, 09 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/fasta2bfa.c
   M /branches/lh3/mapass2/scripts/mapass2.pl

 * 0.4.3-5
 * mapass2.pl: bugfix in SNPfilter
 * fake quality in "fakemut"

------------------------------------------------------------------------
r155 | lh3lh3 | 2007-07-09 18:08:00 +0100 (Mon, 09 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/fasta2bfa.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/pair_stat.cc

 * 0.4.3-4
 * pair_stat.cc: also output depth
 * fasta2bfa.c: fake indels in the reference

------------------------------------------------------------------------
r154 | lh3lh3 | 2007-07-09 11:30:52 +0100 (Mon, 09 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/pair_stat.cc
   M /branches/lh3/mapass2/scripts/mapass2.pl

 * 0.4.3-3
 * pair_stat.cc: skip "N" regions.
 * mapass2.pl: add usage for "SNPfilter"

------------------------------------------------------------------------
r153 | lh3lh3 | 2007-07-08 23:50:10 +0100 (Sun, 08 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/scripts/mapass2.pl

filter SNPs

------------------------------------------------------------------------
r152 | lh3lh3 | 2007-07-08 21:58:21 +0100 (Sun, 08 Jul 2007) | 7 lines
Changed paths:
   M /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/pair_stat.cc
   A /branches/lh3/mapass2/scripts/eval_snp.pl
   M /branches/lh3/mapass2/scripts/mapass2_plot.pl

 * 0.4.3-2
 * add eval_snp.pl
 * mapass2_plot.pl: add depth plot
 * pair_stat.cc: pick up regions that are not covered by pairs
 * aux_utils.c: output alternative depth
 * not finished, though

------------------------------------------------------------------------
r151 | lh3lh3 | 2007-07-06 15:56:18 +0100 (Fri, 06 Jul 2007) | 6 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile.am
   M /branches/lh3/mapass2/Makefile.generic
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   A /branches/lh3/mapass2/pair_stat.cc
   M /branches/lh3/mapass2/scripts/mapass2.pl
   A /branches/lh3/mapass2/scripts/mapass2_plot.pl
   A /branches/lh3/mapass2/simulate.c

 * 0.4.3-1
 * add pair_stat.cc: statistics on paired end data
 * add mapass2_plot.pl: plot utilities
 * mapass2.pl: use find -follow
 * add simulate.c: unfinished

------------------------------------------------------------------------
r147 | lh3lh3 | 2007-07-04 16:04:31 +0100 (Wed, 04 Jul 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/NEWS
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/main.c

Release 0.4.3

------------------------------------------------------------------------
r146 | lh3lh3 | 2007-07-04 14:27:38 +0100 (Wed, 04 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/scripts/farm-run.pl
   M /branches/lh3/mapass2/scripts/mapass2.pl

 * mapass2.pl fastq2bfq: add more descriptions
 * mapass2.pl fastq2bfq: change default number of reads to 1000000
 * farm-run.pl: for easy-to-use

------------------------------------------------------------------------
r145 | lh3lh3 | 2007-07-04 13:51:36 +0100 (Wed, 04 Jul 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/sort_mapping.cc

 * outputing all information with "match -N"
 * 0.4.2-4
 * prepare to release 0.4.3

------------------------------------------------------------------------
r144 | lh3lh3 | 2007-07-03 21:52:34 +0100 (Tue, 03 Jul 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/mapcheck.cc
   M /branches/lh3/mapass2/sort_mapping.cc

 * fix a bug in paired end alignment
 * 0.4.2-3

------------------------------------------------------------------------
r143 | lh3lh3 | 2007-06-29 20:24:11 +0100 (Fri, 29 Jun 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/assopt.c
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/mapcheck.cc
   M /branches/lh3/mapass2/match_aux.cc

 * mapstat: output mapping quality histograph
 * mapcheck: add several command line options and fix two bugs
 * 0.4.2-2

------------------------------------------------------------------------
r142 | lh3lh3 | 2007-06-27 23:43:44 +0100 (Wed, 27 Jun 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/assemble.h
   M /branches/lh3/mapass2/assopt.c
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/get_pos.cc
   M /branches/lh3/mapass2/mapcheck.cc
   M /branches/lh3/mapass2/pileup.cc

 * allow to use single-end mapping qualities
 * check error dependency in mapcheck (testing)
 * 0.4.2-1

------------------------------------------------------------------------
r133 | lh3lh3 | 2007-06-22 14:53:46 +0100 (Fri, 22 Jun 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/scripts/mapass2.pl

 * bugfix: fixed for "mapmerge" when multiple read files are given

------------------------------------------------------------------------
r129 | lh3lh3 | 2007-06-21 16:50:13 +0100 (Thu, 21 Jun 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/NEWS
   M /branches/lh3/mapass2/configure.ac

sorry, a trivial error in version. True Release 0.4.2

------------------------------------------------------------------------
r128 | lh3lh3 | 2007-06-21 16:45:50 +0100 (Thu, 21 Jun 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/NEWS

Release 0.4.2

------------------------------------------------------------------------
r127 | lh3lh3 | 2007-06-21 16:35:35 +0100 (Thu, 21 Jun 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/fasta2bfa.c
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/scripts/mapass2.pl
   M /branches/lh3/mapass2/sort_mapping.cc

 * mapass2.pl: split concatenated paired end reads into two files
 * match command: output read names in stderr
 * 0.4.1-1
 * prepare to release 0.4.2

------------------------------------------------------------------------
r123 | lh3lh3 | 2007-06-17 16:41:14 +0100 (Sun, 17 Jun 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/NEWS
   M /branches/lh3/mapass2/configure.ac

Release 0.4.1

------------------------------------------------------------------------
r122 | lh3lh3 | 2007-06-16 17:22:20 +0100 (Sat, 16 Jun 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/fasta2bfa.c
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h

 * 0.4.0-6
 * randomly mutate a sequence, used for evaluation

------------------------------------------------------------------------
r121 | lh3lh3 | 2007-06-11 16:35:55 +0100 (Mon, 11 Jun 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/scripts/mapass2.pl
   M /branches/lh3/mapass2/sort_mapping.cc

 * recognize "*.fastq.gz" in mapass2.pl
 * record single end quality, but for the moment it has not use.
 * 0.4.0-5

------------------------------------------------------------------------
r120 | lh3lh3 | 2007-06-04 12:52:58 +0100 (Mon, 04 Jun 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/fastq2bfq.c

fix a bug in sol2sanger. Now it should work properly.

------------------------------------------------------------------------
r119 | lh3lh3 | 2007-06-02 17:39:58 +0100 (Sat, 02 Jun 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/fastq2bfq.c
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/read.cc

 * add two commands: sol2sanger and bfq2fastq
 * 0.4.0-3

------------------------------------------------------------------------
r118 | lh3lh3 | 2007-06-01 17:07:58 +0100 (Fri, 01 Jun 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/mapcheck.cc

 * fix a bug in cns2win: when no chr is given, it should report all chrs.
 * allow to change minimum quality at the command-line.
 * in mapcheck, change the default number of mismatches to 4
 * 0.4.0-2

------------------------------------------------------------------------
r117 | lh3lh3 | 2007-06-01 13:52:46 +0100 (Fri, 01 Jun 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/mapcheck.cc

 * fix a bug: bases on the reverse strand are not complemented
 * 0.4.0-1

------------------------------------------------------------------------
r113 | lh3lh3 | 2007-05-15 21:12:51 +0100 (Tue, 15 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/NEWS
   M /branches/lh3/mapass2/README
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/main.c

Release 0.4.0

------------------------------------------------------------------------
r112 | lh3lh3 | 2007-05-15 20:18:47 +0100 (Tue, 15 May 2007) | 6 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/assemble.h
   M /branches/lh3/mapass2/assopt.c
   M /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/get_pos.cc
   M /branches/lh3/mapass2/mapcheck.cc
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/pileup.cc
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/scripts/mapass2.pl

 * Use hash to search sequence names
 * Allow to set a minimum mapping quality when assembling
 * Print out an example of farm-run.pl config
 * 0.3.1-7
 * Prepare to release 0.4.0

------------------------------------------------------------------------
r111 | lh3lh3 | 2007-05-14 22:54:08 +0100 (Mon, 14 May 2007) | 8 lines
Changed paths:
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/configure.ac

 * Hide the alternative model on the command-line. It still works,
   though, and has an accuracy (when -a -t 0.5) quite similar to the
   default one.

 * 0.3.1-6

 * Prepare to release 0.4.0

------------------------------------------------------------------------
r110 | lh3lh3 | 2007-05-14 13:48:28 +0100 (Mon, 14 May 2007) | 10 lines
Changed paths:
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/assopt.c
   M /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/configure.ac

 * Change the default model to $\theta^k$.

 * Forward and reverse strand should be considered together, not
   separately. They are indenpendent in some way, but not totally.

 * The revised model can achieve a similar accuracy in comparison to
   0.3.0.

 * 0.3.1-5

------------------------------------------------------------------------
r109 | lh3lh3 | 2007-05-13 22:51:15 +0100 (Sun, 13 May 2007) | 9 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile.am
   M /branches/lh3/mapass2/Makefile.generic
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/assemble.h
   A /branches/lh3/mapass2/assopt.c
   M /branches/lh3/mapass2/configure.ac
   A /branches/lh3/mapass2/get_pos.cc
   A /branches/lh3/mapass2/mapcheck.cc
   M /branches/lh3/mapass2/match.hh
   A /branches/lh3/mapass2/pileup.cc

 * The consensus calling model is changed again. Like always, the
   performance is worse, but I will still stick to that model.
   Now I feel quite happy with the theory of current model, which
   is the first one that satisfies me.

 * Split assemble.cc into several files.

 * 0.3.1-4

------------------------------------------------------------------------
r108 | lh3lh3 | 2007-05-12 16:04:12 +0100 (Sat, 12 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/INSTALL
   A /branches/lh3/mapass2/Makefile.generic
   D /branches/lh3/mapass2/clean.sh
   A /branches/lh3/mapass2/cleanup.sh (from /branches/lh3/mapass2/clean.sh:107)
   M /branches/lh3/mapass2/main.c

Make without "configuration".

------------------------------------------------------------------------
r107 | lh3lh3 | 2007-05-11 17:21:19 +0100 (Fri, 11 May 2007) | 2 lines
Changed paths:
   A /branches/lh3/mapass2/clean.sh

add a script to clean up all unnecessary files

------------------------------------------------------------------------
r106 | lh3lh3 | 2007-05-11 16:48:52 +0100 (Fri, 11 May 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/INSTALL
   M /branches/lh3/mapass2/Makefile.am
   M /branches/lh3/mapass2/configure.ac

 * 0.3.1-3
 * `make install' now works.
 * INSTALL is updated.

------------------------------------------------------------------------
r105 | lh3lh3 | 2007-05-11 16:26:44 +0100 (Fri, 11 May 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile.am
   M /branches/lh3/mapass2/match_aux.cc

now, mapass2 is known to be compiled under:
i686-linux/x86_64-linux/i386-darwin/i386-Win32/alpha-True64

------------------------------------------------------------------------
r104 | lh3lh3 | 2007-05-11 16:15:45 +0100 (Fri, 11 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/fastq2bfq.c

for TRUE64

------------------------------------------------------------------------
r103 | lh3lh3 | 2007-05-11 15:52:25 +0100 (Fri, 11 May 2007) | 2 lines
Changed paths:
   A /branches/lh3/mapass2/README

add README file

------------------------------------------------------------------------
r102 | lh3lh3 | 2007-05-11 15:48:23 +0100 (Fri, 11 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   D /branches/lh3/mapass2/Makefile
   A /branches/lh3/mapass2/Makefile.am
   D /branches/lh3/mapass2/Makefile.mac
   A /branches/lh3/mapass2/autogen.sh
   A /branches/lh3/mapass2/configure.ac
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/match.cc

use GNU building systems

------------------------------------------------------------------------
r100 | lh3lh3 | 2007-05-10 11:48:06 +0100 (Thu, 10 May 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/sort_mapping.cc

 * 0.3.1-2
 * alignment can be done in color-space

------------------------------------------------------------------------
r99 | lh3lh3 | 2007-05-10 10:18:16 +0100 (Thu, 10 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/aux_utils.c

now SNPs in color-space can be correctly called.

------------------------------------------------------------------------
r98 | lh3lh3 | 2007-05-10 00:22:27 +0100 (Thu, 10 May 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/fasta2bfa.c
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h

 * convert reference to color-space
 * testing command for SNP calling in SOLiD

------------------------------------------------------------------------
r97 | lh3lh3 | 2007-05-09 17:09:50 +0100 (Wed, 09 May 2007) | 2 lines
Changed paths:
   A /branches/lh3/mapass2/Makefile.mac

Makefile for Mac OS X: compiling universal binaries.

------------------------------------------------------------------------
r93 | lh3lh3 | 2007-05-09 13:05:04 +0100 (Wed, 09 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/NEWS

necessary files for release 0.3.1

------------------------------------------------------------------------
r92 | lh3lh3 | 2007-05-09 10:22:23 +0100 (Wed, 09 May 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/NEWS
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/subsnp.cc

 * 0.3.0-5
 * pileup: verbose mode
 * pileup: sub positions
 * reformat NEWS

------------------------------------------------------------------------
r91 | lh3lh3 | 2007-05-08 22:58:57 +0100 (Tue, 08 May 2007) | 7 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/algo.hh
   M /branches/lh3/mapass2/assemble.cc

 - 0.3.0-4
 - fix a memory violation in k-small
 - Modify the consensus calling model. The modified model is more
   correct in theory, but unfortunately with the same command-line
   options this new model yields worse results. However, I will
   use this model. This is my way.

------------------------------------------------------------------------
r90 | lh3lh3 | 2007-05-08 19:12:47 +0100 (Tue, 08 May 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/aux_utils.c

 - 0.3.0-3
 - more options for cns2win

------------------------------------------------------------------------
r89 | lh3lh3 | 2007-05-04 10:55:48 +0100 (Fri, 04 May 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc

 - 0.3.0-2
 - fix a bug when overflow happens given large genome

------------------------------------------------------------------------
r88 | lh3lh3 | 2007-05-04 08:51:21 +0100 (Fri, 04 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/subsnp.cc

add subpos: extract a demanded subset from .cns

------------------------------------------------------------------------
r85 | lh3lh3 | 2007-05-03 09:48:47 +0100 (Thu, 03 May 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/FUTURES
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/NEWS

Necessary files for release

------------------------------------------------------------------------
r84 | lh3lh3 | 2007-05-02 15:31:53 +0100 (Wed, 02 May 2007) | 7 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   A /branches/lh3/mapass2/subsnp.cc


 - 0.2.1-8
 - assemble.cc: fix a bug in calculating avg01match
 - assemble.cc: change default parameters: zita=0.7, max_mm=4
 - subsnp.cc: extract a subset of snps
 - cns2win: information in a window

------------------------------------------------------------------------
r83 | lh3lh3 | 2007-05-02 13:11:57 +0100 (Wed, 02 May 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/algo.hh
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/assemble.h
   M /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/scripts/mapass2.pl

 - 0.2.1-7
 - mapass2.pl: split fastq files and run fastq2bfq in batch
 - save the median and maximum of mapping qualities at a position
 - other codes are modified accordingly

------------------------------------------------------------------------
r82 | lh3lh3 | 2007-04-30 23:37:34 +0100 (Mon, 30 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc

trivial modifications

------------------------------------------------------------------------
r81 | lh3lh3 | 2007-04-30 21:54:34 +0100 (Mon, 30 Apr 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   A /branches/lh3/mapass2/rbcc.cc
   M /branches/lh3/mapass2/scripts/mapass2.pl
   A /branches/lh3/mapass2/stdhash.hh


 - extract main information from dbSNP's chr_rpt.txt
 - add reference based consensus calling method
 - add my hash template class

------------------------------------------------------------------------
r80 | lh3lh3 | 2007-04-30 17:07:05 +0100 (Mon, 30 Apr 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/scripts/mapass2.pl


 - output more information in mapcheck
 - run 'mapcheck' in mapass2.pl

------------------------------------------------------------------------
r79 | lh3lh3 | 2007-04-30 15:53:57 +0100 (Mon, 30 Apr 2007) | 7 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc

Start to use a modified model to call genotypes. The new model
is quite similar to the old one. It does not yield better results
than the old. I change to use this new one just because it is
theoretically meaningful. The old model was designed at the era
of mapass-1 when only the best three bases can be held in the
memory.

------------------------------------------------------------------------
r70 | lh3lh3 | 2007-04-25 16:23:31 +0100 (Wed, 25 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/aux_utils.c

do not output b2_ratio and b3_ratio

------------------------------------------------------------------------
r69 | lh3lh3 | 2007-04-24 21:26:23 +0100 (Tue, 24 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/sort_mapping.cc

revert some of old codes to improve the calculation of paired mapping qualities

------------------------------------------------------------------------
r66 | lh3lh3 | 2007-04-23 23:56:16 +0100 (Mon, 23 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/NEWS

Release 0.2.1

------------------------------------------------------------------------
r65 | lh3lh3 | 2007-04-23 23:31:26 +0100 (Mon, 23 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h

add mapcheck command.

------------------------------------------------------------------------
r64 | lh3lh3 | 2007-04-23 20:00:43 +0100 (Mon, 23 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc

fix a bug in `assemble' when multiple sequences are provided.

------------------------------------------------------------------------
r59 | lh3lh3 | 2007-04-22 20:22:04 +0100 (Sun, 22 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/ChangeLog
   M /branches/lh3/mapass2/FUTURES
   M /branches/lh3/mapass2/INSTALL
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/NEWS

Release mapass2-0.2.0

------------------------------------------------------------------------
r57 | lh3lh3 | 2007-04-22 00:28:15 +0100 (Sun, 22 Apr 2007) | 2 lines
Changed paths:
   A /branches/lh3/mapass2/AUTHORS
   A /branches/lh3/mapass2/COPYING
   A /branches/lh3/mapass2/ChangeLog
   A /branches/lh3/mapass2/FUTURES
   A /branches/lh3/mapass2/INSTALL
   A /branches/lh3/mapass2/NEWS
   A /branches/lh3/mapass2/PROBLEMS

necessary files for release

------------------------------------------------------------------------
r55 | lh3lh3 | 2007-04-21 21:16:28 +0100 (Sat, 21 Apr 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/merge.cc
   M /branches/lh3/mapass2/sort_mapping.cc

 - a few code clean-up, no principal change
 - 0.1.2-11

------------------------------------------------------------------------
r54 | lh3lh3 | 2007-04-21 00:59:11 +0100 (Sat, 21 Apr 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/sort_mapping.cc

 - add back missing read pairs
 - better model to calculate paired quality
 - find abnormal reads
 - 0.1.2-10

------------------------------------------------------------------------
r53 | lh3lh3 | 2007-04-20 10:45:32 +0100 (Fri, 20 Apr 2007) | 10 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/sort_mapping.cc

Finally, I decide to use the new model to calculate mapping qualities. This new
model produce 0.6% more FN+FP at the quality around 20, but it is more
theoretically correct and outperforms the old one at high-quality end. However,
this new model cannot will overestimate qualities when the reads has 3 or more
mismatches. To compensate this, my program now discards reads with 3 or more
mismatches. Surprisingly more or less, this decreases the FP but not increase
FN. We should align reads with "match -n 3" even if we take this strategy.
Allowing more mismatches at the alignment stage helps to calculate better
mapping qualities.

------------------------------------------------------------------------
r52 | lh3lh3 | 2007-04-19 16:34:58 +0100 (Thu, 19 Apr 2007) | 6 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/assemble.h
   M /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/sort_mapping.cc

 - output additional information in .cns
 - 'cns2view': check details for all sites
 - fix a memory violation in assemble.cc
 - attempt to raise the mapping qualities according to my theory, but fail again. The SNPs
   are less accurate.

------------------------------------------------------------------------
r51 | lh3lh3 | 2007-04-19 00:41:48 +0100 (Thu, 19 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/match_aux.cc

do statistics about the .map file

------------------------------------------------------------------------
r50 | lh3lh3 | 2007-04-18 22:58:34 +0100 (Wed, 18 Apr 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/sort_mapping.cc

 - sort_mapping.cc: back ported from r42
 - read.cc: change adaptor quality to zero, instead of masking them

------------------------------------------------------------------------
r49 | lh3lh3 | 2007-04-18 22:28:35 +0100 (Wed, 18 Apr 2007) | 10 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/scripts/farm-run.pl
   M /branches/lh3/mapass2/sort_mapping.cc

All the efforts to implement a "correct" model of mapping quality turn out to
be a complete failure in the end. I still think the current model is correct
when the genome is fully random. However, this is not the truth. Wrong SNPs
tend to arise from the regions where similar sequences existing. My previous
model assumes there is always similar sequences. This is too conservative,
but in practice it works just fine.

What am I going to do next? Probably revert to the old one. I am so frustrating.


------------------------------------------------------------------------
r48 | lh3lh3 | 2007-04-18 13:57:51 +0100 (Wed, 18 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/match.cc

g++-3.3 was complaining this...

------------------------------------------------------------------------
r47 | lh3lh3 | 2007-04-18 11:50:45 +0100 (Wed, 18 Apr 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/read.h

 - allow mismatches when trimming the adaptor sequence
 - even a single base-pair match to the adapator will be masked

------------------------------------------------------------------------
r46 | lh3lh3 | 2007-04-18 00:34:37 +0100 (Wed, 18 Apr 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/const.h
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/read.h

 - dropping adaptor sequences seemingly works
 - I think I should allow mismatches to the adaptor

------------------------------------------------------------------------
r45 | lh3lh3 | 2007-04-17 23:36:07 +0100 (Tue, 17 Apr 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/sort_mapping.cc

 - I was wrong in calculating of mapping quality. I fixed it, but I am afraid that
   we may get more false positives. Anyway, we should stick to the theory, I think.
 - Prepare to add codes to remove the adaptor sequence.

------------------------------------------------------------------------
r42 | lh3lh3 | 2007-04-16 17:12:31 +0100 (Mon, 16 Apr 2007) | 8 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/algo.hh
   M /branches/lh3/mapass2/assemble.cc
   A /branches/lh3/mapass2/aux_utils.c
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   A /branches/lh3/mapass2/scripts
   A /branches/lh3/mapass2/scripts/farm-run.pl
   A /branches/lh3/mapass2/scripts/mapass2.pl
   M /branches/lh3/mapass2/sort_mapping.cc

 - fix a memory leak in assemble.cc
 - fix a bug in algo_heap_adjust(), which subsequently fails 'mapmerge'.
 - output a little more statistics from 'match'
 - add 'cns2snp' and other command to extract information for '.cns' dump
 - add farm-run.pl, my script to facilitate running large jobs on Sanger's farm.
 - add mapass2.pl, a pipeline script
 - 0.1.2-1

------------------------------------------------------------------------
r37 | lh3lh3 | 2007-04-15 22:45:16 +0100 (Sun, 15 Apr 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/match.cc

 - Paired-end data works better, but we need more large-scale test.
 - For some reason, mapass2 is pretty slow on some reads. I have not figured
   out the reason.
 - Prepare to release 0.1.2.

------------------------------------------------------------------------
r35 | lh3lh3 | 2007-04-15 00:05:56 +0100 (Sun, 15 Apr 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   A /branches/lh3/mapass2/sort_mapping.cc

 - put some codes in match_aux.cc into sort_mapping.cc
 - mapview can handle large input files
 - trim_end works again
 - on S. suis data, this version works fine.

------------------------------------------------------------------------
r34 | lh3lh3 | 2007-04-14 18:10:47 +0100 (Sat, 14 Apr 2007) | 6 lines
Changed paths:
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/read.cc

 - just read-pair in the correct way...
 - correct read pair distance
 - high-resolution pair quality (at the cost of memory, though)
 - fix a bug where log_n[] always equals to 0
 - still need more work...

------------------------------------------------------------------------
r33 | lh3lh3 | 2007-04-13 12:41:16 +0100 (Fri, 13 Apr 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/read.cc

 - Paired-end alignment seems to work properly.
 - The next move is to fine tune the matching program.
 - version 0.1.1-2

------------------------------------------------------------------------
r32 | lh3lh3 | 2007-04-12 15:00:18 +0100 (Thu, 12 Apr 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/fastq2bfq.c
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/read.cc
   M /branches/lh3/mapass2/read.h

 - Paired reads should be provided in two files.
 - Automatically find the read length.
 - Codes for paired alignment have been written partly.

------------------------------------------------------------------------
r30 | lh3lh3 | 2007-04-11 17:19:05 +0100 (Wed, 11 Apr 2007) | 3 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc

Mapass2 now works reasonably well for un-paired reads. I will work on paired reads, which
should not be hard in the current frame-work. I will release this single-end version as 0.1.1. 

------------------------------------------------------------------------
r29 | lh3lh3 | 2007-04-10 22:04:25 +0100 (Tue, 10 Apr 2007) | 7 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/algo.hh
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   A /branches/lh3/mapass2/merge.cc


 - Finish "mapmerge" component, which means mapass2 should be able to deal with
   large-scale data such as chrX data.
 - fix a bug: lname was added for several times
 - add heap related functions


------------------------------------------------------------------------
r28 | lh3lh3 | 2007-04-10 16:34:28 +0100 (Tue, 10 Apr 2007) | 2 lines
Changed paths:
   A /branches/lh3/mapass2/assemble.h

I forget this header file...

------------------------------------------------------------------------
r27 | lh3lh3 | 2007-04-10 16:33:46 +0100 (Tue, 10 Apr 2007) | 8 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc


 - output depth in the "pileup" file
 - print 10-based intervals as statistics
 - calculate a little more accurate alignment quality
 - allow to change read-reference difference rate on the command line
 - lower read qualities if mismatches happen at the end of a read
 - on S. suis data, mapass2 can yield similar results to mapass(1)

------------------------------------------------------------------------
r26 | lh3lh3 | 2007-04-10 13:44:54 +0100 (Tue, 10 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/dword.hh
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc

Only hold two index in the memory instead of six. This is a compromise...

------------------------------------------------------------------------
r25 | lh3lh3 | 2007-04-10 11:11:06 +0100 (Tue, 10 Apr 2007) | 6 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/const.c
   M /branches/lh3/mapass2/const.h
   M /branches/lh3/mapass2/match_aux.cc


 - fix a bug when a sequence is reversed.
 - fix a bug for quality mis-calculation
 - The result looks sensible now, but it is not so accurate as the previous
   version. Possibly this is due to the reduced resolution of mapping qualities.

------------------------------------------------------------------------
r24 | lh3lh3 | 2007-04-09 23:31:35 +0100 (Mon, 09 Apr 2007) | 2 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   A /branches/lh3/mapass2/assemble.cc
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc

Add 'pileup' and 'assemble' components. They have not been tested yet.

------------------------------------------------------------------------
r23 | lh3lh3 | 2007-04-04 15:46:16 +0100 (Wed, 04 Apr 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/main.c
   M /branches/lh3/mapass2/main.h
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/read.cc


 - fix maximum mismatch to 4
 - dumping the results is now available
 - 0.1.0-3

------------------------------------------------------------------------
r22 | lh3lh3 | 2007-04-04 13:32:00 +0100 (Wed, 04 Apr 2007) | 4 lines
Changed paths:
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match.hh
   M /branches/lh3/mapass2/match_aux.cc

'match' is a little bit faster, but is still slower than 'mapass'. This is the best I can do for now.
I will move forward to dealing with input/output and consensus calling.


------------------------------------------------------------------------
r21 | lh3lh3 | 2007-04-03 23:19:49 +0100 (Tue, 03 Apr 2007) | 5 lines
Changed paths:
   M /branches/lh3/mapass2/Makefile
   M /branches/lh3/mapass2/match.cc
   M /branches/lh3/mapass2/match_aux.cc
   M /branches/lh3/mapass2/read.cc

Fix three bugs. Now mapass2 can produce the same results on a small example.
However, mapass2 is TOO SLOW!!! I am going to improve it tomorrow. Hope I
can make it... It is so frustrating...


------------------------------------------------------------------------
r18 | lh3lh3 | 2007-04-03 21:08:04 +0100 (Tue, 03 Apr 2007) | 5 lines
Changed paths:
   A /branches/lh3/mapass2
   A /branches/lh3/mapass2/Makefile
   A /branches/lh3/mapass2/algo.hh
   A /branches/lh3/mapass2/bfa.c
   A /branches/lh3/mapass2/bfa.h
   A /branches/lh3/mapass2/const.c
   A /branches/lh3/mapass2/const.h
   A /branches/lh3/mapass2/dword.hh
   A /branches/lh3/mapass2/fasta2bfa.c
   A /branches/lh3/mapass2/fastq2bfq.c
   A /branches/lh3/mapass2/main.c
   A /branches/lh3/mapass2/main.h
   A /branches/lh3/mapass2/match.cc
   A /branches/lh3/mapass2/match.hh
   A /branches/lh3/mapass2/match_aux.cc
   A /branches/lh3/mapass2/read.cc
   A /branches/lh3/mapass2/read.h
   A /branches/lh3/mapass2/seq.c
   A /branches/lh3/mapass2/seq.h

 - New code base. Alignment for paired reads.
 - Streamable alignment file.
 - Non-paired alignment partially works now.


------------------------------------------------------------------------