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UPDATES to BLIMPS programs for Version 3.9
=======================================================================
Outstanding issues:
-Problem with sequences.c:read_a_sequence() if sequence file is rewound
or changed between calls because it saves the last record read.
-Need to call read_a_sequence() to eof after a rewind().
-Should add an initialization flag argument to read_a_sequence() to
force initialization of the buffer.
-Problem reading extremely long title lines of fasta formatted sequences
See include/strutil.h:#define EXTRA_LARGE_BUFF 1000
=======================================================================
Changes since version 3.8:
blimps/protxblk new, lists proteins in blocks
include/protomat.h increased sequence name length from 18 to 20
blimps/blocks.c increased sequence name length
blimps/blalign.c increased sequence name length
blimps/blk2slx.c increased sequence name length
blimps/blkprob.c increased sequence name length
blimps/block_vis.c increased sequence name length
blimps/blweight.c increased sequence name length,
correct number of sequences if necessary
blimps/show_aligned_blocks.c increased sequence name length
blimps/mablock.c increased sequence name length
blimps/format_block.c increased sequence name length
blimps/makelis.c increased sequence name length
protomat/motifj.h increased sequence name length
protomat/motifj.c increased sequence name length
protomat/motomat.c increased sequence name length
protomat/blksort.c increased sequence name length
protomat/multimat.c increased sequence name length
protomat/lislis.c accomodate revised Trembl sequence names
=======================================================================
Changes since version 3.7:
include/protomat.h increased MAXSEQS
protomat/motifj.h increased MAXSEQS
protomat/lislis.c improved sequence name recognition
blimps/addseqs.c improved sequence name recognition
blimps/blklis.c new, read blocks and list sequences
blimps/blDR.c new, rewrite sequences in blocks
bin/osx, lib/osx pre-compiled versions for Mac/OSX
--------------------------------------------------------------------------
Changes since version 3.6:
include/gcode.h: add missing commas to gcodes[] table
affects blimps/gcode.c, blimps/blimps.c and blimps/codehop.c
blimps/block.c, sequences.c: prevent aborts if incomplete blocks
blimps/codehop.h, codehop.c: fixes for genetic codes, incomplete blocks
blimps/blweight.c: increased MAXROWS
protomat/motifj.h: increased MAXSEQS
blimps/papssm.c: new
blimps/convert.c: ignore Xs in blocks when computing scoring matrices,
affects blimps, blk2pssm
lib/libblimps.a: consolidated all libraries into this one
--------------------------------------------------------------------------
Changes since version 3.5:
docs/default.sij removed leading spaces, causes load_qij() to abort!
blimps/addseqs.c compare multi-part sequence names
blimps/blalign.c added Stockholm output format & made it run faster
blimps/blimps.c set error level to suppress most warnings
blimps/blk2pssm.c fixed type argument bug
blimps/blkprob.c use sprintf() instead of kr_itoa,
added -C and -H options
blimps/blocks_search.c new, web page interface
blimps/cobbler.c default values for SU,QM,FR
blimps/convert.c fixed make_alts() problem with types 10,20,21,30
blimps/frequency.c modified error messages
blimps/LAMA.c fixed problem with freeing memory too soon
blimps/mablock.c read Stockholm input format
blimps/makeblockmap.c longer block family name bug
blimps/makelis.c sequence name length problem
blimps/makelogob.c,.h new, makes logos from blocks
blimps/matrix_logob.c data typing problem (added explicit cast)
blimps/pssmdist.c new, calculates theoretical PSSM score distribution
blimps/pssmBL.c new, inserts calibration info from pssmdist in blocks
post-blimps/blksort.c use sprintf() instead of kr_itoa
----------------------------------------------------------------------------
Changes since version 3.4:
blimps/Makefile.Solaris changed compile options to access large files
include/protomat.h added full_entry to struct db_id
include/convert.h SIFT
include/strutil.h EXTRA_LARGE_BUFF for wider blocks
include/gcode.h Updated genetic codes from NCBI
include/protomat.h Increased MAXSEQS and MAXFREQ
blimps/codehop.h Updated list of genetic codes
blimps/blocks.c wider blocks
blimps/protomat.c updates for multi-part sequence names
blimps/cobbler.c fixed bug finding LL sequence in read_seq()
blimps/convert.c added type 22 to block_to_matrix() - almost no pseudos
added type 40 to block_to_matrix() - SIFT
blimps/frequency.c comments
blimps/blweight.c wider blocks
blimps/blpssm.c wider blocks
blimps/mablock.c new parameters, wider blocks, fasta output
blimps/blk2pssm.c new parameters for SIFT, etc.
blimps/rank_matrix.c new program
blimps/bldist.c new program
blimps/narrow.c new program
blimps/prints2blocks.c new program
post-blimps/motifj.h added acc to struct db_info, increased MAXSEQS & MAXFREQ
post-blimps/motmisc.c changes for multi-part sequence names
post-blimps/uextract.c changed lis_list() to print id->full_entry
added -k option
post-blimps/blksort.c fixed bug when hit vs blocks with > MAXSEQS seqs
docs/default.sij, default.diri new for SIFT
www/ Blocks Server html files - samples only
=======================================================================
Solaris: Compile to access large (>2gb) files "man lfcompile"
Change ftell() to ftello() and fseek() to fseeko()
then
cc `getconf LFS_CFLAGS` -fast ... -ly
|
