------------------------------------------------------------------------
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...

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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()

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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.


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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

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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

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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

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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

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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. :)


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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

------------------------------------------------------------------------
