Package detail

bionode-bwa

bionode17MIT2.0.0

A Node.js wrapper for the Burrow-Wheeler Aligner (BWA).

bio, biology, bionode, bioinformatics, aligner, wrapper, installer, streams, cli

readme

bionode.io

# bionode-bwa > A Node.js wrapper for the Burrow-Wheeler Aligner (BWA).

Install

Install bionode-bwa with npm:

$ npm install bionode-bwa

To use it as a command line tool, you can install it globally by adding -g .

Usage

If you're using bionode-bwa with Node.js, you can require the module:

var bwa = require('bionode-bwa')
// aligment path is optional, reads name used instead with sam suffix
bwa('reference.fasta.gz', 'reads.fastq.gz', 'alignment.sam')
.on('data', console.log)

var options = {
  operation: 'mem',
  params: '-t 4'
}
var stream = bwa(options) // Use BWA mem algorithm with 4 threads
var obj = {
  reference: 'reference.fasta.gz',
  reads: ['reads.fastq.gz']
}
stream.write(obj)

Please read the documentation for the methods exposed by bionode-bwa.
Check BWA's documentation for the arguments that can be passed.

Command line examples

$ bionode-bwa reference.fasta.gz reads.fastq.gz --alignment out.sam
$ echo '{"reference": "ref.fasta.gz", "reads": "[p1.fq, p2.fq]"}' | bionode-bwa  -

Contributing

To contribute, clone this repo locally and commit your code on a separate branch.

Please write unit tests for your code, and check that everything works by running the following before opening a pull-request:

$ npm test

Please also check for code coverage:

$ npm run coverage

To rebuild the documentation using the comments in the code:

$ npm run build-docs

Check the issues for ways to contribute.

Contacts

Bruno Vieira <mail@bmpvieira.com> @bmpvieira
For BWA support contact Heng Li

License

bionode-bwa is licensed under the MIT license.
Check ChooseALicense.com for details.

changelog

r1605 | lh3 | 2010-12-29 20:20:20 -0500 (Wed, 29 Dec 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.5.9rc1-2 (r1605)
fixed a typo/bug in bwasw

r1587 | lh3 | 2010-12-21 18:48:30 -0500 (Tue, 21 Dec 2010) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

a typo in the manual

r1586 | lh3 | 2010-12-21 18:47:48 -0500 (Tue, 21 Dec 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c M /branches/prog/bwa/utils.c M /branches/prog/bwa/utils.h

bwa-0.5.9rc1-1 (r1586)
a few patches by John

r1562 | lh3 | 2010-12-10 01:02:06 -0500 (Fri, 10 Dec 2010) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c

documentation on specifying @RG

r1561 | lh3 | 2010-12-10 00:45:40 -0500 (Fri, 10 Dec 2010) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.5.9rc1 (r1561)

r1560 | lh3 | 2010-12-10 00:29:08 -0500 (Fri, 10 Dec 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/main.c

fixed a small memory leak caused by the BAM reader
fixed a memory violation, also in the BAM reader

r1559 | lh3 | 2010-12-10 00:10:48 -0500 (Fri, 10 Dec 2010) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/Makefile

change Makefile gcc options

r1558 | lh3 | 2010-12-10 00:09:22 -0500 (Fri, 10 Dec 2010) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.5.8-6 (r1557)
added a little more comments to BWA-SW
randomly choosing a mapping if there are more than one

r1557 | lh3 | 2010-12-09 21:58:00 -0500 (Thu, 09 Dec 2010) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2_aux.c

sometimes unmapped reads may not be printed...

r1556 | lh3 | 2010-12-09 21:50:26 -0500 (Thu, 09 Dec 2010) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2_aux.c

print unmapped reads

r1555 | lh3 | 2010-12-09 21:17:20 -0500 (Thu, 09 Dec 2010) | 3 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.5.8-5 (r1555)
BAM input documentation

r1544 | lh3 | 2010-11-23 11:01:41 -0500 (Tue, 23 Nov 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.5.8-4 (r1544)
supporting adding RG tags and RG lines

r1543 | lh3 | 2010-11-23 00:16:40 -0500 (Tue, 23 Nov 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.5.8-3 (r1543)
fixed a memory leak

r1542 | lh3 | 2010-11-22 23:50:56 -0500 (Mon, 22 Nov 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.5.8-2 (r1542)
fixed a long existing bug in random placement of reads

r1541 | lh3 | 2010-11-22 23:27:29 -0500 (Mon, 22 Nov 2010) | 2 lines Changed paths: M /branches/prog/bwa/Makefile A /branches/prog/bwa/bamlite.c A /branches/prog/bwa/bamlite.h M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

preliminary BAM input support

r1537 | lh3 | 2010-10-16 23:46:20 -0400 (Sat, 16 Oct 2010) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwa.1

change version number and ChangeLog

r1536 | lh3 | 2010-10-16 23:35:10 -0400 (Sat, 16 Oct 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c

fixed a bug in the scoring matrix
release bwa-0.5.8c (r1536)

r1451 | lh3 | 2010-06-15 09:43:52 -0400 (Tue, 15 Jun 2010) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

version change

r1450 | lh3 | 2010-06-15 09:42:21 -0400 (Tue, 15 Jun 2010) | 3 lines Changed paths: M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c

bwa-0.5.8b (r1450)
fixed a bug in scoring matrix

r1445 | lh3 | 2010-06-11 08:58:33 -0400 (Fri, 11 Jun 2010) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c

fixed a serious bug

r1442 | lh3 | 2010-06-08 10:22:14 -0400 (Tue, 08 Jun 2010) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.5.8 (r1442)

r1440 | lh3 | 2010-05-19 13:43:50 -0400 (Wed, 19 May 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-r1440
sorry, forget to remove a debugging line

r1439 | lh3 | 2010-05-19 13:43:08 -0400 (Wed, 19 May 2010) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-r1439
fixed a bug in bwasw caused by a recent modification
throwing insane insert size when estimating isize

r1425 | lh3 | 2010-04-29 15:15:23 -0400 (Thu, 29 Apr 2010) | 10 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.5.7-7 (r1425)
fixed a minor bug in bwasw command-line parsing
When band-width is not large enough, bwasw may find two highly overlapping but not completely overlapping alignments. The old version will filter out one of them, which leads to false negatives. The current outputs both. This solution is obviously not ideal. The ideal one would be to increase the band-width and redo the alignment.

r1399 | lh3 | 2010-04-16 09:20:49 -0400 (Fri, 16 Apr 2010) | 3 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.5.7-6 (r1399)
fixed a typo/bug (by Vaughn Iverson)

r1329 | lh3 | 2010-03-19 23:32:46 -0400 (Fri, 19 Mar 2010) | 2 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

small correction

r1328 | lh3 | 2010-03-19 23:28:44 -0400 (Fri, 19 Mar 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.5.7-4 (r1328)
automatically adjust ap_prior based on alignment

r1327 | lh3 | 2010-03-19 23:02:40 -0400 (Fri, 19 Mar 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.5.7-3 (r1327)
evaluate hits obtained from SW alignment in a more proper way.

r1320 | lh3 | 2010-03-17 15:13:22 -0400 (Wed, 17 Mar 2010) | 2 lines Changed paths: M /branches/prog/bwa/bwape.c

fixed a potential out-of-boundary error. Need more testing.

r1319 | lh3 | 2010-03-14 22:44:46 -0400 (Sun, 14 Mar 2010) | 2 lines Changed paths: M /branches/prog/bwa/bwape.c

insert size is `weird' if the 3rd quatile larger than 100,000bp

r1318 | lh3 | 2010-03-14 22:37:35 -0400 (Sun, 14 Mar 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.5.7-2 (r1318)
in sampe, allow to disable insert size estimate

r1317 | lh3 | 2010-03-14 22:14:14 -0400 (Sun, 14 Mar 2010) | 5 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c M /branches/prog/bwa/solid2fastq.pl

bwa-0.5.7-1 (r1317)
fixed a potential bug in solid2fastq.pl
fixed a bug in calculating mapping quality (by Rodrigo Goya)
fixed a very rare bug (if ever occur) about pairing

r1310 | lh3 | 2010-03-01 10:35:45 -0500 (Mon, 01 Mar 2010) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.5.7

r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.5.6-2 (r1309)
fixed an unfixed bug (by Carol Scott)
fixed some tiny formatting

r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.5.6-1 (r1304)
optionally write output to a file (by Tim Fennel)

r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

Release bwa-0.5.6

r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.5.5-10 (r1302)
improve max insert size estimate (method suggested by Gerton Lunter)

r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.5.5-9 (r1301)
improve mapping quality calculation for abnomalous pairs
fixed a bug in multiple hits
SOLiD multiple hits should work now

r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.5.5-8 (r1300)
output kurtosis

r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.5.5-7 (r1299)
calculate skewness in sampe
increase min_len in SW to 20
perform more SW to fix discordant pairs

r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/cs2nt.c M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.h

bwa-0.5.5-6 (r1297)
prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya)

r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines Changed paths: M /branches/prog/bwa/solid2fastq.pl

the old fix seems not working!

r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.5.5-5 (r1296)
fixed a minor issue that the lower bound of insert size is not correctly set.

r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/main.c

bwa-0.5.5-4 (r1295)
fixed a memory leak
change the behaviour of -n (samse and sampe)
change the default of -n

r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.5.5-3 (r1294)
improved multi-hit report

r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/cs2nt.c M /branches/prog/bwa/main.c M /branches/prog/bwa/solid2fastq.pl

bwa-0.5.5-2 (r1293)
bugfix: truncated quality string
bugfix: quality -1 in solid->fastq conversion
bugfix: color reads on the reverse strand is not complemented

r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bntseq.h M /branches/prog/bwa/bwase.c A /branches/prog/bwa/bwase.h M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.5.5-1 (r1279)
incorporate changes from Matt Hanna for Java bindings.

r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog

update ChangeLog

r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c A /branches/prog/bwa/qualfa2fq.pl

Release bwa-0.5.5 (r1273)

r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.5.4-3 (r1272)
fixed another typo which may lead to incorrect single-end mapping quality

r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.5.4-2 (r1271)
fixed a serious typo/bug which does not hurt if we allow one gap open and work with <200bp reads, but causes segfault for long reads.

r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines Changed paths: M /branches/prog/bwa/cs2nt.c M /branches/prog/bwa/main.c

bwa-0.5.4-1 (r1270)
fixed a bug in color alignment

r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/main.c

Release bwa-0.5.4

r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c

bwa-0.5.3-4 (r1244)
output the clipped length in XC:i: tag
skip mate alignment when stdaln is buggy
fixed a bug in NM:i: tag

r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.5.3-3 (r1243)
sampe: fixed a bug when a read sequence is identical its reverse complement.

r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.5.3-2 (r1242)
sampe: optionall preload the full index into memory
aln: change the default seed length to 32bp

r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines Changed paths: M /branches/prog/bwa/khash.h

Improve portability of khash.h

r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines Changed paths: M /branches/prog/bwa/main.c

fixed a typo

r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.5.3-1 (r1226)
in dBWT-SW, optionall use hard clipping instead of soft clipping

r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

Release bwa-0.5.3 (r1225)

r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.5.2

r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.5.1-5 (r1222)
fixed a typo. No real change

r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.5.1-4 (r1221)
trim reads before alignment

r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.5.1-3 (r1216)
fixed a bug about NM tags for gapped alignment
print SAM header

r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.5.1-2 (r1215)
fixed a bug when read lengths vary (by John Marshall)

r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.5.1-1 (r1213)
change default -T to 30

r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.5.1

r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog

ChangeLog

r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.5.0-6 (r1206)
fixed two bugs caused by previous modification

r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.5.0-4 (r1205)
reduce false coordinates and CIGAR when a query bridges two reference sequences, although some very rare cases may fail bwa.

r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.5.0-3 (r1204)
choose one repetitive hit to extend

r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.5.0-2 (r1203)
dBWT-SW: change a parameter in calculating mapping quality
fixed a bug in samse

r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.5.0-1 (r1202)
change default band width to 50
improve mapping quality a bit

r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.5.0 (r1200)

r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwa.1

Updated ChangeLog and the manual

r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-36 (r1198)
simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse.

r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2_aux.c A /branches/prog/bwa/bwtsw2_chain.c M /branches/prog/bwa/main.c

bwa-0.4.9-35 (r1197)
further heuristic acceleration for long queries

r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.4.9-34 (r1196)
updated the manual page
output base quality if the input is fastq

r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c M /branches/prog/bwa/simple_dp.c

bwa-0.4.9-33 (r1191)
fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment
in dbwtsw adjust -T and -c according to -a

r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update manual

r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwtsw2_main.c

update documentation

r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-32 (r1190)
only help messages are changed

r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-31 (r1189)
in bwape/bwase, print CIGAR "*" if the read is unmapped
improved the calculation of mapping quality

r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c

fflush()

r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.4.9-30 (r1180)
fixed a memory problem
multi-threading sometimes does not work...

r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-29 (r1179)
preliminary mutli-threading support in dbwtsw

r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-28 (r1178)
fixed a bug in printing repetitive hits

r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-27 (r1177)
bwtsw2: fixed a hidden memory leak

r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-26
change the way mapping quality is calculated

r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-25
code clean up
automatically adjust ->t and ->is_rev based on input

r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/main.c

bwa-0.4.9-24
fixed a bug in printing the hits

r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-23
allow to skip reverse alignment
increase opt->t to 37

r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-22
report if the hit is found in both directions

r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-21
dbwtsw: map to both forward and reverse BWT to reduce false alignment

r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

save hits before cut_tail()

r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.4.9-19
use a global memory pool to reduce the CPU time spent on malloc/free().

r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-18
reduce unnecessary extension to the 5'-end
allow to use different interval size for the 2 rounds
change default parameters

r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-17
dbwtsw: fixed THE memory leak.

r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c

bwa-0.4.9-16
fixed a memory leak
a small memory leak still occurs to bwtsw2_core(). I will work on that later.
changed the default parameters

r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c

bwa-0.4.9-15
generate CIGAR right before output. This saves unnecessary computation.
this version may be buggy as I have not tested it.

r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.4.9-14
deplete unique hits in dbwtsw and postprocess them with standard sw
in principle, this stratgy should be faster and more accurate, but I have not tested this point. I may switch back to the old method if this does not work.
the code looks quite nasty now. it needs clean up...

r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c

change a default parameter

r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-13
dbwtsw: switch between small and large Z-best

r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-12
changed the default -z to 100
heuristically speed up alignments for polyA reads

r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-11
dbwtsw potentially generates less false alignments, although in practice, the modification brings no improvement.

r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-10
disabled debugging code
add "BAM_FMU" if both ends are unmapped

r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/main.c

nothing, really

r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-9
bwtsw2: generate SAM output

r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.4.9-8
fixed a weird deadloop which only happens to icc -O3. Thanks John Marshall for the fix.

r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-7
fixed a typo in bwtsw2 alignment. Now score from the standard SW seems to agree with score from bwtsw2, except that in reporting alignments, bwtsw2 may report non-optimal segments. This is expected, though. I will improve in future.

r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

aln_left_core() seems to work properly
aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!!

r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/stdaln.c

removed debugging code...

r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/stdaln.c

radical changes failed...
fixed a bug

r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/stdaln.c

temporary changes. Will apply some radical changes to this file...

r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/stdaln.c

fixed a long-existing bug in Smith-Waterman alignment

r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c M /branches/prog/bwa/simple_dp.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.4.9-6
unexplained inconsistency still occurs, but the results largely look reasonable.

r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/stdaln.c

half DP

r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c

a bit code clean up

r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-5
fixed a bug in determining sub-optimal hits
removed some debugging codes

r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.4.9-4
better cmd interface
faster speed

r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwtsw2 (dBWT-SW) is working apparently...

r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.4.9-2
bwtsw2: change cut_tail() such that it is faster but more likely to miss true hits

r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines Changed paths: M /branches/prog/bwa/Makefile A /branches/prog/bwa/bwt_lite.c A /branches/prog/bwa/bwt_lite.h A /branches/prog/bwa/bwtsw2.h A /branches/prog/bwa/bwtsw2_aux.c A /branches/prog/bwa/bwtsw2_core.c A /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

bwa-0.4.9-1
added back bwtsw2

r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

Release bwa-0.4.9

r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.4.8

r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.4.7-2
change the default of "aln -R" to 30

r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.4.7-1
search for suboptimal hits if the top hit is not so repetitive

r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

Release bwa-0.4.7

r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.6-9
fixed compiling errors on some Linux machines

r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.4.6-8
avoid compilation error on some systems.

r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.6-7
fixed an integer overflow caused by previous modifications
made insert size estimation more robust

r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.6-5
fixed a integer overflow problem which may cause seg fault in very rare cases
made XN tags more accurate

r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c M /branches/prog/bwa/simple_dp.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.4.6-4
heuristic rules to detect suboptimal alignment
stdsw: support double-strand and protein alignment

r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines Changed paths: M /branches/prog/bwa/main.c M /branches/prog/bwa/simple_dp.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.4.6-2
improve the functionality of stdsw
allow to add a threshold on SW alignment. Hope this does not incur new bugs...

r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.4.6-1
output SM and AM tag

r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.4.6

r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c A /branches/prog/bwa/solid2fastq.pl

added notes to bwa
added a script to convert SOLiD reads
updated documentations

r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/kstring.c M /branches/prog/bwa/main.c

fixed a bug in kstring

r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtmisc.c M /branches/prog/bwa/main.c

bwa-0.4.5-7
fixed a bug in pac2cspac

r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines Changed paths: M /branches/prog/bwa/Makefile

disable debugging

r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/cs2nt.c M /branches/prog/bwa/main.c

bwa-0.4.5-6
fixed problems with coordinates for color gapped alignment

r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/cs2nt.c M /branches/prog/bwa/main.c

bwa-0.4.5-5
added support for gapped color alignment

r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/cs2nt.c M /branches/prog/bwa/main.c

convert cs read to nt read (for ungapped alignment only)

r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwase.c A /branches/prog/bwa/cs2nt.c

prepare to implement cs->nt conversion (have not yet...)

r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bntseq.h M /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/bwtmisc.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

bwa-0.4.5-3
generate color index from nucleotide fasta reference

r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.4.5-2
improved mapping quality a bit if one end falls in a tandem repeat but the mate is unique.

r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.4.5-1
make bwa work for SOLiD reads

r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.4.5

r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/main.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.4.4-6
fixed a bug in SW alignment when no residue matches

r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.4.4-5
fixed that bounary bug

r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwape.c

just change some logging information

r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update manual

r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.4-4
fixed a bug on boundary check in pair_sw

r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.4.4-3
allow to change mismatch penalty

r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.4.4-2
remove timer
allow to change default gapo and gape penalty at the command line

r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update benchmark

r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/kvec.h M /branches/prog/bwa/main.c

bwa-0.4.4-1
automatically detect insert size
use insert size in pairing. This may potentially improve accuracy (untested!)

r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.4.4

r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.3-5
impose boundary check in refine_gapped

r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.3-4
change MD tag to match the latest SAM specification

r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog

update ChangeLog

r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

change MD tag to meet the latest SAM specification

r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.3-2
fixed a bug on counting 'N'

r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.4.3-1
fixed potential boundary problems
update benchmark result

r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update some numbers

r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update benchmark

r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwtindex.c

a warning message for index

r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/main.c

forget to change release number

r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/NEWS

Release bwa-0.4.3

r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS

Release bwa-0.4.3

r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.2-10
update documentation
fixed a bug on generating MD tags for SW alignment

r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.2-9
fixed a bug in samse -n...

r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.4.2-8
given -N, the previous version would stop if the top hit is a repeat. Now changed.

r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.4.2-7
use a bit-wise flag to replace some member variables in the option struct
allow to switch off the iterative strategy

r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.2-6
allow to dump multiple hits from samse, in another format, though

r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/kseq.h A /branches/prog/bwa/kstring.c A /branches/prog/bwa/kstring.h M /branches/prog/bwa/main.c M /branches/prog/bwa/simple_dp.c

bwa-0.4.2-5
update kseq.h to the latest version
generate MD tag
print mate coordinate if only one end is unmapped

r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.4.2-4
fixed a bug for SAM format

r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.4.2-3
change default fnr to 0.04
print max_diff for valid fnr

r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.4.2-2
automatically choose max_diff

r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.4.2-1
take N as a mismatch

r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/main.c

Release bwa-0.4.2

r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

Release bwa-0.4.1

r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.4.0-2
make mate_sw fully working

r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.4.0-1
do SW alignment for unmapped mate. It is working.
I still need to do some extra work for SW alignment, but it is too late and I am getting tired... I will do tomorrow.

r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.4.0

r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtgap.h M /branches/prog/bwa/main.c

bwa-0.3.0-12
better lock

r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.3.0-11
fixed a small memory leak in bwa_seq_close()
fixed "uninitialized memory" from bwt_aln1_t
multithreading for "aln" command

r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/Makefile D /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwt_gen/bwt_gen.c A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748) M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h D /branches/prog/bwa/pac2bwt.c

bwa-0.3.0-10
a little bit code clean up

r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.3.0-9
use 64-bit integer to speed up Occ calculate, although just a little bit

r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.3.0-8
a little bit code cleanup

r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.1.0-7
accelerate Occ calculation

r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h M /branches/prog/bwa/pac2bwt.c

bwa-0.3.0-6
put occ table along with bwt to save another cache miss
this version is already faster than the previous and I can still improve it...

r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/main.c

bwa-0.3.0-5
remove occ_major to save a cache miss; however, OCC_INTERVAL has to be increased to keep the same memory. As a result, the speed is a little slower in fact.

r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.3.0-4
added back optimization codes (it is a pain...)

r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.3.0-3
faster bit operations

r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.3.0-2
removed optimization codes again...
use a new method to count the bits

r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.3.0-1
added back the optimization codes
added a new option to aln: max_entries, although this is disabled by default
updated benchmark

r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

add URL

r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.3.0

r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines Changed paths: A /branches/prog/bwa/COPYING M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bntseq.h M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/utils.c M /branches/prog/bwa/utils.h

added licensing information

r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.2.0-31
better mapping quality
update benchmark

r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwa.1

update documentation

r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update documentation

r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.2.0-30
reduce memory a little bit
update documentation

r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines Changed paths: M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.2.0-29
sampe: removed -O option; changed default -o to 100000
sampe: fixed a bug in calculating paired mapping quality
aln: added an option to search for suboptimal hits even if the best is a repeat. This option will make sampe MUCH SLOWER.
sampe: set isize as zero if mapped to two different chr
update manual (unfinished)

r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/main.c

bwa-0.2.0-28
fixed a bug in calculating paired mapping quality

r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675) M /branches/prog/bwa/main.c

bwa-0.2.0-27
accelerate sampe by storing visited large intervals

r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.2.0-26
remove the optimation codes

r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.2.0-25
accelerate OCC calculation by ~7%. However, it seems not worth doing this by complicate the codes. I will change back later.

r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.2.0-24
change command "sai2sam_pe" to "sampe"
print usage for sampe command
in sampe: change default max_occ to 1000
fixed a few compiling warnings in bntseq.c

r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/main.c

bwa-0.2.0-22
mating information can be printed to SAM

r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.2.0-21
implement pairing (still UNFINISHED)
output all reads even if full of N

r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines Changed paths: M /branches/prog/bwa/Makefile A /branches/prog/bwa/bwape.c M /branches/prog/bwa/bwase.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

bwa-0.2.0-20
remove "-t" from aln cmd
code clean up: move some functions in bwt2fmv.c to other source files
added sai2sam_pe cmd: UNFINISHED

r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile A /branches/prog/bwa/bwase.c A /branches/prog/bwa/bwaseqio.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/kseq.h A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712) A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537) M /branches/prog/bwa/main.c

bwa-0.2.0-19
considerable code cleanup; no actual changes

r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.2.0-18
generate SAM output

r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

bwa-0.2.0-17
remove bwtsw2 related codes
separate searching for SA interval from generating alignments

r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt2fmv.c D /branches/prog/bwa/bwt_lite.c D /branches/prog/bwa/bwt_lite.h M /branches/prog/bwa/bwtgap.c D /branches/prog/bwa/bwtsw2.h D /branches/prog/bwa/bwtsw2_aux.c D /branches/prog/bwa/bwtsw2_core.c D /branches/prog/bwa/bwtsw2_main.c D /branches/prog/bwa/khash.h D /branches/prog/bwa/ksort.h D /branches/prog/bwa/kvec.h M /branches/prog/bwa/main.c

added interface to "aln -t"
remove bwtsw2 related codes

r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.2.0-16
allow to set max mismatches based on read length, but I do not know whether this really works

r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.2.0-15
fixed a bug in sequence parser.

r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/main.c M /branches/prog/bwa/utils.c

bwa-0.2.0-14
fixed a bug caused by the change of the FASTA/Q parser

r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bntseq.h M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtsw2_core.c A /branches/prog/bwa/kseq.h D /branches/prog/bwa/seq.c D /branches/prog/bwa/seq.h M /branches/prog/bwa/simple_dp.c M /branches/prog/bwa/utils.c M /branches/prog/bwa/utils.h

replace seq.* with kseq.h

r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.2.0-13
make bwtsw2 output sub-optimal hits. not completed

r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines Changed paths: M /branches/prog/bwa/kvec.h

little...

r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/khash.h

improve interface of khash

r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

improve minor things, which make bwtsw2 slower, but should miss less true hits

r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

fixed a bug in calculating ->D
enforce band-width checking

r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

delete a line of code that is never visited

r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

a bit code clean up

r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.2.0-12
max-depth can be set, although it does not help the speed at all

r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

cut_tail after remove duplicate

r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/khash.h M /branches/prog/bwa/main.c

bwa-0.2.0-11
improved cut_tail()

r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.2.0-10
fixed a bug in cut_tail()

r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

a bit code clean up

r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

improve speed (<1%)

r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

fixed two potential bugs, although I have not seen their effects
improve speed a bit (<2%)

r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c

nothing, really

r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

disable X-drop, which has to be reimplemented in the current algorithm

r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt_lite.c M /branches/prog/bwa/bwt_lite.h M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c

temporarily disable cut_tail()
calculate SA in bwt_lite.c
fixed a bug in reversing the sequence

r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c A /branches/prog/bwa/ksort.h

n-best method

r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2_core.c

give correct result again

r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

I think I know the reason. It needs more work...

r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2_core.c

fixed another bug, but still have

r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

fixed another bug

r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/khash.h

do not segfault, but the result is WRONG!
prepare to remove bsw2_connectivity_check()

r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/kvec.h

more revisions

r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

further simply codes with kvec.h

r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

part of revisions... have not finished

r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/khash.h A /branches/prog/bwa/kvec.h

prepare for abrupt change

r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

fixed a bug; now "bwtsw2 -d" is useless

r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/simple_dp.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

improve speed a little bit

r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

remove debug codes

r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

improve the speed a little bit (<5%)
prepare to remove BSW_DEBUG

r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.2.0-9
support reverse strand
fixed a bug that causes missing hits

r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.2.0-8
better progress report

r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.2.0-7
avoid some missing hits
add maximum depth

r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/main.c

bwa-0.2.0-6
bwtsw2 works although on the forward strand only for now
better progress information

r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

implement memory pool
avoid some rehashing

r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_main.c

fixed a memory leak
prepare to implement mempool

r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/khash.h

add X-dropoff
remove duplicated results
switch to simple stack

r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c

check whether t-node has been visited
prepare to remove two-level stack

r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines Changed paths: A /branches/prog/bwa/khash.h

khash library

r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

add inline

r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c

improve speed

r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtsw2_core.c

Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just keep a copy in case I may need this in future.

r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_core.c

no principal modification

r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2_core.c

fixed a bug which may cause duplicated matching
accelerate the speed a bit, although using hash in avoiding duplications slows the speed down in the end

r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtsw2.h M /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.2.0-5
indel seems to work on toy example
add band

r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt_lite.c M /branches/prog/bwa/bwt_lite.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtsw2.h A /branches/prog/bwa/bwtsw2_aux.c M /branches/prog/bwa/bwtsw2_core.c M /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/is.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h M /branches/prog/bwa/simple_dp.c

bwa-0.2.0-4
updated bwtsw2, which seems to work properly on toy examples

r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.2.0-3
tune for longer gaps, but it does not really work with kilo-bp gaps...

r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.2.0-2
changed the way to extend long deletions. Now use max_del_occ.

r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt_lite.c M /branches/prog/bwa/bwt_lite.h

updated from bwtsw2_lite

r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.h A /branches/prog/bwa/bwt_lite.c A /branches/prog/bwa/bwt_lite.h A /branches/prog/bwa/bwtsw2.h A /branches/prog/bwa/bwtsw2_core.c A /branches/prog/bwa/bwtsw2_main.c M /branches/prog/bwa/main.c

bwa-0.2.0-1
add bwt_lite: a light-weighted version of bwt (NOT TESTED!)
add core codes for bwtsw2: NOT TESTED!!!

r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

Release bwa-0.2.0

r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c

bwa-0.1.6-7
change default seed length to 31
add incomplete support to color sequences (not tested yet!)

r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.1.6-6
change default seed length to 33bp

r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.1.6-5
fixed a bug that may miss true alignments. this bugs exists in most early versions.
fixed a bug that yields wrong coordinates for reads mapped on the forward strands with gaps.

r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines Changed paths: D /branches/prog/bwa/Makefile.div

useless

r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.1.6-4
fixed one bug
there is another one...

r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtgap.h M /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/main.c

bwa-0.1.6-3
almost there, but not quite right

r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtgap.h M /branches/prog/bwa/main.c

improve the seeding method
prepare to load two BWTs into memory. A BIG change!

r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtgap.h M /branches/prog/bwa/main.c

added seeding
unfinished yet

r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.1.6

r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines Changed paths: M /branches/prog/bwa/simple_dp.c

sw: output alignment score

r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h A /branches/prog/bwa/simple_dp.c M /branches/prog/bwa/stdaln.c M /branches/prog/bwa/stdaln.h

bwa-0.1.5-3
added a simple interface to SW/NW alignment
stdaln-0.9.8 (see header for more details)

r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c A /branches/prog/bwa/stdaln.c A /branches/prog/bwa/stdaln.h

bwa-0.1.5-2
give accurate gap positions

r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h

unfinished, but I am tired...

r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/main.c

bwa-0.1.5-1
fixed a potential bug which may produce an alignment in N regions, although extremely rare.

r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.1.5

r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update documentation

r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.1.4-4
add timer for debugging

r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.1.4-3
fixed a bug in the previous code
this version gives identical result to bwa-0.1.4, just 10% faster

r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtgap.h M /branches/prog/bwa/main.c

bwa-0.1.4-2
further improve the speed
The result is slightly different from bwa-0.1.4 now. I need to check...

r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt.c

comments only

r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

further improve the speed in Occ functions

r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/main.c

Release bwa-0.1.4

r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwa.1

update documentation and ChangeLog

r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.1.3-2
fixed the bug in the last modification
now the alignment should be more clearly defined

r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.1.3-1
this is a buggy verion!
i will fix the bug tomorrow. It is late...

r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.1.3

r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/ChangeLog M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/main.c

bwa-0.1.2-3
improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux
aln: more command-line options

r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/main.c

bwa-0.1.2-2
further improve the speed
this version gives exactly the same result as bwa-0.1.2

r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/main.c

bwa-0.1.2-1
speed up by about 5%

r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.1.2

r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile D /branches/prog/bwa/bwt1away.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtgap.h D /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.1-9
some code cleanup
remove 1away and top2

r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines Changed paths: M /branches/prog/bwa/is.c

Yuta Mori's implementation of IS algorithm.

r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwtgap.h M /branches/prog/bwa/main.c

bwa-0.1.1-8
improve gapped alignment
this version will miss more gapped alignments, but the speed is much faster
prepare to remove top2 and 1away algorithms
prepare to add SAIS algorithm for bwt construction

r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.1.1-7
change END_SKIP from 3 to 5, but still gaps may be wrongly added
change default '-g' from 5 to 3

r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.1.1-6
fix a bug in nested stack

r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c A /branches/prog/bwa/bwtgap.h M /branches/prog/bwa/main.c

bwa-0.1.1-5
replace heap with nested stacks
there are still obvious bugs...

r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

bwa-0.1.1-4
add interface to affine gap alignment
there are obvious bugs and I will fix them later

r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/main.c

bwa-0.1.1-3
affine gap seems to work, at least partially

r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h A /branches/prog/bwa/bwtgap.c M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.1-2
initial gapped alignment. not work at the moment

r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.1-1
ungap: remove a useless varible in top2_entry_t

r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines Changed paths: M /branches/prog/bwa/ChangeLog A /branches/prog/bwa/NEWS M /branches/prog/bwa/bwa.1 M /branches/prog/bwa/main.c

Release bwa-0.1.1

r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwa.1

update documentation

r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines Changed paths: A /branches/prog/bwa/ChangeLog A /branches/prog/bwa/bwa.1 M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.1.0-11
improve approximating mapping qualities
add documentation
add ChangeLog

r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.0-10
output a random position for repetitive reads

r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c M /branches/prog/bwa/pac2bwt.c

bwa-0.1.0-9
fix memory leaks
fix a potential bug in coverting to the real coordinate

r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines Changed paths: M /branches/prog/bwa/Makefile.div M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.0-8
fix a bug about strand
update Makefile.div
change top2b as the default method

r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt1away.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c

bwa-0.1.0-7
use bwt_2occ() and bwt_2occ4() in other functions

r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.0-6
fix a bug for missing hits

r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.0-5
accelerate comparisons in heap, a bit

r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.0-4
avoid marginal repeated calculation in occ

r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.0-3
fix a bug caused by previours change
fix a bug in heap
order the heap by more criteria

r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c

bwa-0.1.0-2
also sort sa range in heapsort, in attempt to improve cache performance. Unfortunately, it does not work well at all.

r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/Makefile.div M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/main.c

0.1.0-1
fix a bug in calculating the real coordinate

r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile

nothing, really

r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile A /branches/prog/bwa/Makefile.div M /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/pac2bwt.c

use IS algorithm by default

r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/is.c M /branches/prog/bwa/pac2bwt.c

a bit code clean up in is.c
add IS algorithm for constructing BWT, albeit slower

r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines Changed paths: A /branches/prog/bwa/is.c

IS linear-time algorithm for constructing SA/BWT

r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bntseq.c A /branches/prog/bwa/bwtindex.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

fix a bug in generating .pac
index in one go

r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bntseq.h M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwttop2.c

real coordinates can be ouput

r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwttop2.c

add top2e which is similar to 1away

r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwttop2.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

unified cmd-line interface for ungapped alignment
add two alternatives to top2 algorithm

r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

add cmd-line interface to alntop2

r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt1away.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h A /branches/prog/bwa/bwttop2.c

top2 algorithm seems to work. I need to change interface, though

r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt1away.c

change the variable in the structure

r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt1away.c

set a slightly better bound on the maximum allowed mismatches

r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwtaln.c

output time statistics

r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h A /branches/prog/bwa/bwt1away.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h

presumably better way to make use of prefix. But for the moment I do not know whether it is correct or not.
a bit code clean up: separate alignment part

r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt_gen/Makefile M /branches/prog/bwa/bwt_gen/bwt_gen.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h M /branches/prog/bwa/pac2bwt.c

a bit code clean up
put bwt_gen in bwa

r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtio.c

improve cmd-line interface
fix a bug in loading .sa
change default sa interval to 32

r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwtaln.c

fix memory leak (I know that. Just a bit lazy)
change to another method to do 1-away alignment

r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

best unique match is partially finished

r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

remove "ungapped" command and related codes

r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h

change variable name thick to width

r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h M /branches/prog/bwa/pac2bwt.c

revised algorithm for ungapped alignment. the old one can still be used.

r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwt_gen/bwt_gen.c M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/pac2bwt.c

make commands more independent, but ungapped does not work at the moment

r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt_gen/bwt_gen.c

little...

r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt_gen/bwt_gen.c M /branches/prog/bwa/bwt_gen/bwt_gen.h

add CopyRight information from the original codes
do not dump .fmv files

r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines Changed paths: A /branches/prog/bwa/bwt_gen A /branches/prog/bwa/bwt_gen/Makefile A /branches/prog/bwa/bwt_gen/QSufSort.c A /branches/prog/bwa/bwt_gen/QSufSort.h A /branches/prog/bwa/bwt_gen/bwt_gen.c A /branches/prog/bwa/bwt_gen/bwt_gen.h

codes from BWT-SW, for building BWT from packed file

r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

change OCC_INTERVAL to 0x40, which makes bwa twice as fast.
write Occ file as ".occ" as it is using a different interval from .fmv, the BWT-SW correspondance of .occ

r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt2fmv.c

fix a bug

r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt2fmv.c

add heuristics to improve the speed, but I have not tested whether the results are correct or not.

r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/bwtaln.c M /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

make ungapped alignment basically works...
but it is very slow in comparison to others...
also I need to improve the interface...
a lot of things to keep me busy today...

r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwtaln.c

remove recursion
fixed a bug in bwt_occ()

r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines Changed paths: M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwtaln.c

bwa now tells whether a sequenced can be mapped with maximum allowed mismatches. ONLY ungapped.
this is a recursive version. I will remove recursion later.

r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c A /branches/prog/bwa/bwtaln.c A /branches/prog/bwa/bwtaln.h M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h M /branches/prog/bwa/utils.c

load .sa and .fmv files
exact alignment now works

r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwtio.c M /branches/prog/bwa/utils.c M /branches/prog/bwa/utils.h

add xassert and fix a bug

r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwtio.c A /branches/prog/bwa/utils.c A /branches/prog/bwa/utils.h

improve error message and error handling

r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c A /branches/prog/bwa/bwtio.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h

move I/O codes to bwtio.c
SA can be dumped and interestingly, it is identical to BWTSW
now, .fmv is still different from BWTSW

r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c

generate/retrieve SA and Occ

r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines Changed paths: M /branches/prog/bwa/bntseq.h M /branches/prog/bwa/bwt.c M /branches/prog/bwa/bwt.h M /branches/prog/bwa/bwt2fmv.c

retrieve occ value at any position
move bwt_cal_occ() to bwt.c

r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines Changed paths: M /branches/prog/bwa/Makefile A /branches/prog/bwa/bwt.c A /branches/prog/bwa/bwt.h A /branches/prog/bwa/bwt2fmv.c M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h M /branches/prog/bwa/pac2bwt.c

add bwt2fmv. It works to some extend. However, I do not understand the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv could generate a file almost identical, but not exactly identical, to the .fmv file from BWT-SW.

r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines Changed paths: M /branches/prog/bwa/Makefile M /branches/prog/bwa/bntseq.c M /branches/prog/bwa/bntseq.h M /branches/prog/bwa/main.c M /branches/prog/bwa/main.h A /branches/prog/bwa/pac2bwt.c

Burrows-Wheeler Transform now works. At least on one example, the current code generates the same BWT as BWT-SW. Kind of magical, I would say. :)

r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines Changed paths: A /branches/prog/bwa/Makefile M /branches/prog/bwa/bntseq.c A /branches/prog/bwa/main.c A /branches/prog/bwa/main.h

add Makefile and main.*
improve interface to fa2bns, a bit

r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines Changed paths: A /branches/prog/bwa A /branches/prog/bwa/bntseq.c A /branches/prog/bwa/bntseq.h A /branches/prog/bwa/seq.c A /branches/prog/bwa/seq.h

Burrow-Wheeler Alignment
initial codes