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ChangeLog
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ChangeLog
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------------------------------------------------------------------------
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