bio-bwa 0.2.0

data/ext/ChangeLog

@@ -0,0 +1,3864 @@
+------------------------------------------------------------------------
+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
+
+------------------------------------------------------------------------