File: UPDATES

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blimps 3.9+ds-1
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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