Mercurial > repos > siyuan > prada
diff pyPRADA_1.2/tools/bwa-0.5.7-mh/ChangeLog @ 0:acc2ca1a3ba4
Uploaded
| author | siyuan |
|---|---|
| date | Thu, 20 Feb 2014 00:44:58 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/ChangeLog Thu Feb 20 00:44:58 2014 -0500 @@ -0,0 +1,3545 @@ +------------------------------------------------------------------------ +r1309 | lh3 | 2010-02-26 21:42:22 -0500 (Fri, 26 Feb 2010) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.5.6-2 (r1309) + * fixed an unfixed bug (by Carol Scott) + * fixed some tiny formatting + +------------------------------------------------------------------------ +r1305 | lh3 | 2010-02-25 13:47:58 -0500 (Thu, 25 Feb 2010) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.5.6-1 (r1304) + * optionally write output to a file (by Tim Fennel) + +------------------------------------------------------------------------ +r1303 | lh3 | 2010-02-10 23:43:48 -0500 (Wed, 10 Feb 2010) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + +Release bwa-0.5.6 + +------------------------------------------------------------------------ +r1302 | lh3 | 2010-02-10 11:11:49 -0500 (Wed, 10 Feb 2010) | 3 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.5.5-10 (r1302) + * improve max insert size estimate (method suggested by Gerton Lunter) + +------------------------------------------------------------------------ +r1301 | lh3 | 2010-02-09 16:15:28 -0500 (Tue, 09 Feb 2010) | 5 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.5.5-9 (r1301) + * improve mapping quality calculation for abnomalous pairs + * fixed a bug in multiple hits + * SOLiD multiple hits should work now + +------------------------------------------------------------------------ +r1300 | lh3 | 2010-02-09 12:50:02 -0500 (Tue, 09 Feb 2010) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.5.5-8 (r1300) + * output kurtosis + +------------------------------------------------------------------------ +r1299 | lh3 | 2010-02-09 12:33:34 -0500 (Tue, 09 Feb 2010) | 5 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.5.5-7 (r1299) + * calculate skewness in sampe + * increase min_len in SW to 20 + * perform more SW to fix discordant pairs + +------------------------------------------------------------------------ +r1298 | lh3 | 2010-02-08 12:40:31 -0500 (Mon, 08 Feb 2010) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/cs2nt.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.5.5-6 (r1297) + * prepare to replace all 16-bit CIGAR (patches by Rodrigo Goya) + +------------------------------------------------------------------------ +r1297 | lh3 | 2010-02-05 22:26:11 -0500 (Fri, 05 Feb 2010) | 2 lines +Changed paths: + M /branches/prog/bwa/solid2fastq.pl + +the old fix seems not working! + +------------------------------------------------------------------------ +r1296 | lh3 | 2010-02-05 21:51:03 -0500 (Fri, 05 Feb 2010) | 3 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.5.5-5 (r1296) + * fixed a minor issue that the lower bound of insert size is not correctly set. + +------------------------------------------------------------------------ +r1295 | lh3 | 2010-02-05 21:01:10 -0500 (Fri, 05 Feb 2010) | 5 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/main.c + + * bwa-0.5.5-4 (r1295) + * fixed a memory leak + * change the behaviour of -n (samse and sampe) + * change the default of -n + +------------------------------------------------------------------------ +r1294 | lh3 | 2010-02-05 17:24:06 -0500 (Fri, 05 Feb 2010) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.5.5-3 (r1294) + * improved multi-hit report + +------------------------------------------------------------------------ +r1293 | lh3 | 2010-02-05 12:57:38 -0500 (Fri, 05 Feb 2010) | 5 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/cs2nt.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/solid2fastq.pl + + * bwa-0.5.5-2 (r1293) + * bugfix: truncated quality string + * bugfix: quality -1 in solid->fastq conversion + * bugfix: color reads on the reverse strand is not complemented + +------------------------------------------------------------------------ +r1279 | lh3 | 2009-11-23 22:42:34 -0500 (Mon, 23 Nov 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bntseq.h + M /branches/prog/bwa/bwase.c + A /branches/prog/bwa/bwase.h + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.5.5-1 (r1279) + * incorporate changes from Matt Hanna for Java bindings. + +------------------------------------------------------------------------ +r1275 | lh3 | 2009-11-10 22:13:10 -0500 (Tue, 10 Nov 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + +update ChangeLog + +------------------------------------------------------------------------ +r1273 | lh3 | 2009-11-10 22:08:16 -0500 (Tue, 10 Nov 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + A /branches/prog/bwa/qualfa2fq.pl + +Release bwa-0.5.5 (r1273) + +------------------------------------------------------------------------ +r1272 | lh3 | 2009-11-10 22:02:50 -0500 (Tue, 10 Nov 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.5.4-3 (r1272) + * fixed another typo which may lead to incorrect single-end mapping quality + +------------------------------------------------------------------------ +r1271 | lh3 | 2009-11-10 21:59:47 -0500 (Tue, 10 Nov 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.5.4-2 (r1271) + * fixed a serious typo/bug which does not hurt if we allow one gap open + and work with <200bp reads, but causes segfault for long reads. + +------------------------------------------------------------------------ +r1270 | lh3 | 2009-11-09 23:12:42 -0500 (Mon, 09 Nov 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/cs2nt.c + M /branches/prog/bwa/main.c + + * bwa-0.5.4-1 (r1270) + * fixed a bug in color alignment + +------------------------------------------------------------------------ +r1245 | lh3 | 2009-10-09 07:42:52 -0400 (Fri, 09 Oct 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/main.c + +Release bwa-0.5.4 + +------------------------------------------------------------------------ +r1244 | lh3 | 2009-10-09 05:53:52 -0400 (Fri, 09 Oct 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + M /branches/prog/bwa/stdaln.c + + * bwa-0.5.3-4 (r1244) + * output the clipped length in XC:i: tag + * skip mate alignment when stdaln is buggy + * fixed a bug in NM:i: tag + +------------------------------------------------------------------------ +r1243 | lh3 | 2009-10-07 08:15:04 -0400 (Wed, 07 Oct 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.5.3-3 (r1243) + * sampe: fixed a bug when a read sequence is identical its reverse complement. + +------------------------------------------------------------------------ +r1242 | lh3 | 2009-10-07 07:49:13 -0400 (Wed, 07 Oct 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.5.3-2 (r1242) + * sampe: optionall preload the full index into memory + * aln: change the default seed length to 32bp + +------------------------------------------------------------------------ +r1238 | lh3 | 2009-09-26 18:38:15 -0400 (Sat, 26 Sep 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/khash.h + +Improve portability of khash.h + +------------------------------------------------------------------------ +r1228 | lh3 | 2009-09-15 09:20:22 -0400 (Tue, 15 Sep 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/main.c + +fixed a typo + +------------------------------------------------------------------------ +r1227 | lh3 | 2009-09-15 09:19:35 -0400 (Tue, 15 Sep 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.5.3-1 (r1226) + * in dBWT-SW, optionall use hard clipping instead of soft clipping + +------------------------------------------------------------------------ +r1225 | lh3 | 2009-09-15 08:32:30 -0400 (Tue, 15 Sep 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + +Release bwa-0.5.3 (r1225) + +------------------------------------------------------------------------ +r1223 | lh3 | 2009-09-13 07:30:41 -0400 (Sun, 13 Sep 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.5.2 + +------------------------------------------------------------------------ +r1222 | lh3 | 2009-09-11 09:11:39 -0400 (Fri, 11 Sep 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.5.1-5 (r1222) + * fixed a typo. No real change + +------------------------------------------------------------------------ +r1221 | lh3 | 2009-09-11 09:09:44 -0400 (Fri, 11 Sep 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.5.1-4 (r1221) + * trim reads before alignment + +------------------------------------------------------------------------ +r1216 | lh3 | 2009-09-08 17:50:15 -0400 (Tue, 08 Sep 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.5.1-3 (r1216) + * fixed a bug about NM tags for gapped alignment + * print SAM header + +------------------------------------------------------------------------ +r1215 | lh3 | 2009-09-08 17:14:42 -0400 (Tue, 08 Sep 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.5.1-2 (r1215) + * fixed a bug when read lengths vary (by John Marshall) + +------------------------------------------------------------------------ +r1213 | lh3 | 2009-09-06 18:58:15 -0400 (Sun, 06 Sep 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.5.1-1 (r1213) + * change default -T to 30 + +------------------------------------------------------------------------ +r1209 | lh3 | 2009-09-02 06:06:02 -0400 (Wed, 02 Sep 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.5.1 + +------------------------------------------------------------------------ +r1208 | lh3 | 2009-09-02 05:56:33 -0400 (Wed, 02 Sep 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + + * ChangeLog + +------------------------------------------------------------------------ +r1206 | lh3 | 2009-08-30 18:27:30 -0400 (Sun, 30 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.5.0-6 (r1206) + * fixed two bugs caused by previous modification + +------------------------------------------------------------------------ +r1205 | lh3 | 2009-08-30 17:28:36 -0400 (Sun, 30 Aug 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.5.0-4 (r1205) + * reduce false coordinates and CIGAR when a query bridges two reference + sequences, although some very rare cases may fail bwa. + +------------------------------------------------------------------------ +r1204 | lh3 | 2009-08-30 06:06:16 -0400 (Sun, 30 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.5.0-3 (r1204) + * choose one repetitive hit to extend + +------------------------------------------------------------------------ +r1203 | lh3 | 2009-08-29 18:11:51 -0400 (Sat, 29 Aug 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.5.0-2 (r1203) + * dBWT-SW: change a parameter in calculating mapping quality + * fixed a bug in samse + +------------------------------------------------------------------------ +r1202 | lh3 | 2009-08-28 19:48:41 -0400 (Fri, 28 Aug 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.5.0-1 (r1202) + * change default band width to 50 + * improve mapping quality a bit + +------------------------------------------------------------------------ +r1200 | lh3 | 2009-08-20 06:21:24 -0400 (Thu, 20 Aug 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/main.c + +Release bwa-0.5.0 (r1200) + +------------------------------------------------------------------------ +r1199 | lh3 | 2009-08-20 04:49:15 -0400 (Thu, 20 Aug 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bwa.1 + +Updated ChangeLog and the manual + +------------------------------------------------------------------------ +r1198 | lh3 | 2009-08-19 11:09:15 -0400 (Wed, 19 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-36 (r1198) + * simplify duphits removal. The accuracy is changed a tiny bit, sometimes better, sometimes worse. + +------------------------------------------------------------------------ +r1197 | lh3 | 2009-08-19 08:15:05 -0400 (Wed, 19 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtsw2_aux.c + A /branches/prog/bwa/bwtsw2_chain.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-35 (r1197) + * further heuristic acceleration for long queries + +------------------------------------------------------------------------ +r1196 | lh3 | 2009-08-18 06:54:03 -0400 (Tue, 18 Aug 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-34 (r1196) + * updated the manual page + * output base quality if the input is fastq + +------------------------------------------------------------------------ +r1195 | lh3 | 2009-08-18 06:23:00 -0400 (Tue, 18 Aug 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/simple_dp.c + + * bwa-0.4.9-33 (r1191) + * fixed a bug in sampe/samse when gaps occur to the 5'-end in SW alignment + * in dbwtsw adjust -T and -c according to -a + +------------------------------------------------------------------------ +r1192 | lh3 | 2009-08-13 05:37:28 -0400 (Thu, 13 Aug 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update manual + +------------------------------------------------------------------------ +r1191 | lh3 | 2009-08-12 19:40:51 -0400 (Wed, 12 Aug 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwtsw2_main.c + +update documentation + +------------------------------------------------------------------------ +r1190 | lh3 | 2009-08-12 08:56:10 -0400 (Wed, 12 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-32 (r1190) + * only help messages are changed + +------------------------------------------------------------------------ +r1189 | lh3 | 2009-08-11 09:28:55 -0400 (Tue, 11 Aug 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-31 (r1189) + * in bwape/bwase, print CIGAR "*" if the read is unmapped + * improved the calculation of mapping quality + +------------------------------------------------------------------------ +r1181 | lh3 | 2009-08-03 12:09:41 -0400 (Mon, 03 Aug 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + +fflush() + +------------------------------------------------------------------------ +r1180 | lh3 | 2009-08-03 12:08:46 -0400 (Mon, 03 Aug 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-30 (r1180) + * fixed a memory problem + * multi-threading sometimes does not work... + +------------------------------------------------------------------------ +r1179 | lh3 | 2009-08-03 11:04:39 -0400 (Mon, 03 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-29 (r1179) + * preliminary mutli-threading support in dbwtsw + +------------------------------------------------------------------------ +r1178 | lh3 | 2009-08-03 09:14:54 -0400 (Mon, 03 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-28 (r1178) + * fixed a bug in printing repetitive hits + +------------------------------------------------------------------------ +r1177 | lh3 | 2009-08-03 05:03:42 -0400 (Mon, 03 Aug 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-27 (r1177) + * bwtsw2: fixed a hidden memory leak + +------------------------------------------------------------------------ +r1176 | lh3 | 2009-07-31 10:58:24 -0400 (Fri, 31 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-26 + * change the way mapping quality is calculated + +------------------------------------------------------------------------ +r1175 | lh3 | 2009-07-31 09:15:54 -0400 (Fri, 31 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-25 + * code clean up + * automatically adjust ->t and ->is_rev based on input + +------------------------------------------------------------------------ +r1174 | lh3 | 2009-07-30 08:50:25 -0400 (Thu, 30 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-24 + * fixed a bug in printing the hits + +------------------------------------------------------------------------ +r1173 | lh3 | 2009-07-29 18:32:43 -0400 (Wed, 29 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-23 + * allow to skip reverse alignment + * increase opt->t to 37 + +------------------------------------------------------------------------ +r1172 | lh3 | 2009-07-29 17:22:39 -0400 (Wed, 29 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-22 + * report if the hit is found in both directions + +------------------------------------------------------------------------ +r1171 | lh3 | 2009-07-29 17:12:02 -0400 (Wed, 29 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-21 + * dbwtsw: map to both forward and reverse BWT to reduce false alignment + +------------------------------------------------------------------------ +r1170 | lh3 | 2009-07-29 15:25:14 -0400 (Wed, 29 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + +save hits before cut_tail() + +------------------------------------------------------------------------ +r1169 | lh3 | 2009-07-29 08:06:01 -0400 (Wed, 29 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.4.9-19 + * use a global memory pool to reduce the CPU time spent on malloc/free(). + +------------------------------------------------------------------------ +r1168 | lh3 | 2009-07-29 06:13:29 -0400 (Wed, 29 Jul 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-18 + * reduce unnecessary extension to the 5'-end + * allow to use different interval size for the 2 rounds + * change default parameters + +------------------------------------------------------------------------ +r1167 | lh3 | 2009-07-28 19:06:17 -0400 (Tue, 28 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-17 + * dbwtsw: fixed THE memory leak. + +------------------------------------------------------------------------ +r1166 | lh3 | 2009-07-28 16:31:41 -0400 (Tue, 28 Jul 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/stdaln.c + + * bwa-0.4.9-16 + * fixed a memory leak + * a small memory leak still occurs to bwtsw2_core(). I will work on that later. + * changed the default parameters + +------------------------------------------------------------------------ +r1165 | lh3 | 2009-07-28 10:15:40 -0400 (Tue, 28 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/stdaln.c + + * bwa-0.4.9-15 + * generate CIGAR right before output. This saves unnecessary computation. + * this version may be buggy as I have not tested it. + +------------------------------------------------------------------------ +r1164 | lh3 | 2009-07-28 09:04:14 -0400 (Tue, 28 Jul 2009) | 11 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.4.9-14 + + * deplete unique hits in dbwtsw and postprocess them with standard sw + + * in principle, this stratgy should be faster and more accurate, but I + have not tested this point. I may switch back to the old method if + this does not work. + + * the code looks quite nasty now. it needs clean up... + + +------------------------------------------------------------------------ +r1163 | lh3 | 2009-07-27 17:41:10 -0400 (Mon, 27 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + +change a default parameter + +------------------------------------------------------------------------ +r1162 | lh3 | 2009-07-27 17:04:35 -0400 (Mon, 27 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-13 + * dbwtsw: switch between small and large Z-best + +------------------------------------------------------------------------ +r1161 | lh3 | 2009-07-27 12:17:41 -0400 (Mon, 27 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-12 + * changed the default -z to 100 + * heuristically speed up alignments for polyA reads + +------------------------------------------------------------------------ +r1160 | lh3 | 2009-07-27 07:50:57 -0400 (Mon, 27 Jul 2009) | 6 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-11 + + * dbwtsw potentially generates less false alignments, although in + practice, the modification brings no improvement. + + +------------------------------------------------------------------------ +r1159 | lh3 | 2009-07-27 04:37:02 -0400 (Mon, 27 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-10 + * disabled debugging code + * add "BAM_FMU" if both ends are unmapped + +------------------------------------------------------------------------ +r1158 | lh3 | 2009-07-24 09:36:52 -0400 (Fri, 24 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/main.c + +nothing, really + +------------------------------------------------------------------------ +r1157 | lh3 | 2009-07-24 09:05:44 -0400 (Fri, 24 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-9 + * bwtsw2: generate SAM output + +------------------------------------------------------------------------ +r1156 | lh3 | 2009-07-24 05:42:47 -0400 (Fri, 24 Jul 2009) | 6 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-8 + + * fixed a weird deadloop which only happens to icc -O3. Thanks John + Marshall for the fix. + + +------------------------------------------------------------------------ +r1155 | lh3 | 2009-07-24 05:28:40 -0400 (Fri, 24 Jul 2009) | 8 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-7 + + * fixed a typo in bwtsw2 alignment. Now score from the standard SW + seems to agree with score from bwtsw2, except that in reporting + alignments, bwtsw2 may report non-optimal segments. This is expected, + though. I will improve in future. + + +------------------------------------------------------------------------ +r1154 | lh3 | 2009-07-23 17:40:20 -0400 (Thu, 23 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * aln_left_core() seems to work properly + * aln_local_core() has a bug... AN EVER EXISTING BUG!!!!!!!!!!! + +------------------------------------------------------------------------ +r1153 | lh3 | 2009-07-23 17:06:09 -0400 (Thu, 23 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/stdaln.c + +removed debugging code... + +------------------------------------------------------------------------ +r1152 | lh3 | 2009-07-23 17:01:00 -0400 (Thu, 23 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/stdaln.c + + * radical changes failed... + * fixed a bug + +------------------------------------------------------------------------ +r1151 | lh3 | 2009-07-23 14:46:35 -0400 (Thu, 23 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/stdaln.c + +temporary changes. Will apply some radical changes to this file... + +------------------------------------------------------------------------ +r1150 | lh3 | 2009-07-23 10:09:56 -0400 (Thu, 23 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/stdaln.c + +fixed a long-existing bug in Smith-Waterman alignment + +------------------------------------------------------------------------ +r1149 | lh3 | 2009-07-23 08:50:52 -0400 (Thu, 23 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/simple_dp.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.4.9-6 + * unexplained inconsistency still occurs, but the results largely look reasonable. + +------------------------------------------------------------------------ +r1148 | lh3 | 2009-07-23 08:07:29 -0400 (Thu, 23 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/stdaln.c + +half DP + +------------------------------------------------------------------------ +r1147 | lh3 | 2009-07-22 08:03:06 -0400 (Wed, 22 Jul 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + +a bit code clean up + +------------------------------------------------------------------------ +r1145 | lh3 | 2009-07-21 15:52:05 -0400 (Tue, 21 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-5 + * fixed a bug in determining sub-optimal hits + * removed some debugging codes + +------------------------------------------------------------------------ +r1144 | lh3 | 2009-07-21 10:17:29 -0400 (Tue, 21 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-4 + * better cmd interface + * faster speed + +------------------------------------------------------------------------ +r1143 | lh3 | 2009-07-20 16:38:18 -0400 (Mon, 20 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + +bwtsw2 (dBWT-SW) is working apparently... + + +------------------------------------------------------------------------ +r1139 | lh3 | 2009-07-15 05:52:18 -0400 (Wed, 15 Jul 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.4.9-2 + * bwtsw2: change cut_tail() such that it is faster but more likely to + miss true hits + +------------------------------------------------------------------------ +r1138 | lh3 | 2009-07-15 05:18:42 -0400 (Wed, 15 Jul 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + A /branches/prog/bwa/bwt_lite.c + A /branches/prog/bwa/bwt_lite.h + A /branches/prog/bwa/bwtsw2.h + A /branches/prog/bwa/bwtsw2_aux.c + A /branches/prog/bwa/bwtsw2_core.c + A /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * bwa-0.4.9-1 + * added back bwtsw2 + +------------------------------------------------------------------------ +r1075 | lh3 | 2009-05-19 05:14:50 -0400 (Tue, 19 May 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + +Release bwa-0.4.9 + +------------------------------------------------------------------------ +r1073 | lh3 | 2009-05-18 17:13:19 -0400 (Mon, 18 May 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.4.8 + +------------------------------------------------------------------------ +r1069 | lh3 | 2009-05-14 09:54:54 -0400 (Thu, 14 May 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.4.7-2 + * change the default of "aln -R" to 30 + +------------------------------------------------------------------------ +r1068 | lh3 | 2009-05-14 09:27:55 -0400 (Thu, 14 May 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.4.7-1 + * search for suboptimal hits if the top hit is not so repetitive + +------------------------------------------------------------------------ +r1066 | lh3 | 2009-05-12 15:31:31 -0400 (Tue, 12 May 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + +Release bwa-0.4.7 + +------------------------------------------------------------------------ +r1065 | lh3 | 2009-05-12 15:20:40 -0400 (Tue, 12 May 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.6-9 + * fixed compiling errors on some Linux machines + +------------------------------------------------------------------------ +r1064 | lh3 | 2009-05-12 07:30:46 -0400 (Tue, 12 May 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.4.6-8 + * avoid compilation error on some systems. + +------------------------------------------------------------------------ +r1035 | lh3 | 2009-05-09 05:41:33 -0400 (Sat, 09 May 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.6-7 + * fixed an integer overflow caused by previous modifications + * made insert size estimation more robust + +------------------------------------------------------------------------ +r1008 | lh3 | 2009-04-29 05:41:58 -0400 (Wed, 29 Apr 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.6-5 + * fixed a integer overflow problem which may cause seg fault in very rare cases + * made XN tags more accurate + +------------------------------------------------------------------------ +r1005 | lh3 | 2009-04-27 07:37:23 -0400 (Mon, 27 Apr 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/simple_dp.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.4.6-4 + * heuristic rules to detect suboptimal alignment + * stdsw: support double-strand and protein alignment + +------------------------------------------------------------------------ +r1003 | lh3 | 2009-04-26 12:48:19 -0400 (Sun, 26 Apr 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/main.c + M /branches/prog/bwa/simple_dp.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.4.6-2 + * improve the functionality of stdsw + * allow to add a threshold on SW alignment. Hope this does not incur new bugs... + +------------------------------------------------------------------------ +r1002 | lh3 | 2009-04-22 03:56:15 -0400 (Wed, 22 Apr 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.4.6-1 + * output SM and AM tag + +------------------------------------------------------------------------ +r914 | lh3 | 2009-03-09 17:53:50 -0400 (Mon, 09 Mar 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/main.c + +Release bwa-0.4.6 + +------------------------------------------------------------------------ +r913 | lh3 | 2009-03-09 17:23:24 -0400 (Mon, 09 Mar 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + A /branches/prog/bwa/solid2fastq.pl + + * added notes to bwa + * added a script to convert SOLiD reads + * updated documentations + +------------------------------------------------------------------------ +r912 | lh3 | 2009-03-09 16:57:05 -0400 (Mon, 09 Mar 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/kstring.c + M /branches/prog/bwa/main.c + +fixed a bug in kstring + +------------------------------------------------------------------------ +r881 | lh3 | 2009-03-02 15:36:06 -0500 (Mon, 02 Mar 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtmisc.c + M /branches/prog/bwa/main.c + + * bwa-0.4.5-7 + * fixed a bug in pac2cspac + +------------------------------------------------------------------------ +r880 | lh3 | 2009-03-01 16:34:08 -0500 (Sun, 01 Mar 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + +disable debugging + +------------------------------------------------------------------------ +r879 | lh3 | 2009-03-01 16:28:04 -0500 (Sun, 01 Mar 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/cs2nt.c + M /branches/prog/bwa/main.c + + * bwa-0.4.5-6 + * fixed problems with coordinates for color gapped alignment + +------------------------------------------------------------------------ +r878 | lh3 | 2009-03-01 13:43:09 -0500 (Sun, 01 Mar 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/cs2nt.c + M /branches/prog/bwa/main.c + + * bwa-0.4.5-5 + * added support for gapped color alignment + +------------------------------------------------------------------------ +r877 | lh3 | 2009-03-01 10:27:52 -0500 (Sun, 01 Mar 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/cs2nt.c + M /branches/prog/bwa/main.c + + * convert cs read to nt read (for ungapped alignment only) + +------------------------------------------------------------------------ +r860 | lh3 | 2009-02-27 08:58:39 -0500 (Fri, 27 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwase.c + A /branches/prog/bwa/cs2nt.c + +prepare to implement cs->nt conversion (have not yet...) + +------------------------------------------------------------------------ +r859 | lh3 | 2009-02-27 07:00:03 -0500 (Fri, 27 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bntseq.h + M /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/bwtmisc.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * bwa-0.4.5-3 + * generate color index from nucleotide fasta reference + +------------------------------------------------------------------------ +r857 | lh3 | 2009-02-26 10:22:58 -0500 (Thu, 26 Feb 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.4.5-2 + * improved mapping quality a bit if one end falls in a tandem repeat + but the mate is unique. + +------------------------------------------------------------------------ +r856 | lh3 | 2009-02-26 10:02:29 -0500 (Thu, 26 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.4.5-1 + * make bwa work for SOLiD reads + +------------------------------------------------------------------------ +r828 | lh3 | 2009-02-18 17:36:41 -0500 (Wed, 18 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.4.5 + +------------------------------------------------------------------------ +r827 | lh3 | 2009-02-18 16:48:48 -0500 (Wed, 18 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/main.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.4.4-6 + * fixed a bug in SW alignment when no residue matches + +------------------------------------------------------------------------ +r824 | lh3 | 2009-02-17 05:33:07 -0500 (Tue, 17 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.4.4-5 + * fixed that bounary bug + +------------------------------------------------------------------------ +r823 | lh3 | 2009-02-17 04:54:18 -0500 (Tue, 17 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bwape.c + +just change some logging information + +------------------------------------------------------------------------ +r822 | lh3 | 2009-02-17 04:20:39 -0500 (Tue, 17 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update manual + +------------------------------------------------------------------------ +r821 | lh3 | 2009-02-17 04:11:14 -0500 (Tue, 17 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.4-4 + * fixed a bug on boundary check in pair_sw + +------------------------------------------------------------------------ +r820 | lh3 | 2009-02-16 17:43:37 -0500 (Mon, 16 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.4.4-3 + * allow to change mismatch penalty + +------------------------------------------------------------------------ +r819 | lh3 | 2009-02-16 17:40:28 -0500 (Mon, 16 Feb 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.4.4-2 + * remove timer + * allow to change default gapo and gape penalty at the command line + +------------------------------------------------------------------------ +r818 | lh3 | 2009-02-16 09:30:51 -0500 (Mon, 16 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update benchmark + +------------------------------------------------------------------------ +r817 | lh3 | 2009-02-16 08:44:40 -0500 (Mon, 16 Feb 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/kvec.h + M /branches/prog/bwa/main.c + + * bwa-0.4.4-1 + * automatically detect insert size + * use insert size in pairing. This may potentially improve accuracy (untested!) + +------------------------------------------------------------------------ +r814 | lh3 | 2009-02-15 11:10:23 -0500 (Sun, 15 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/main.c + +Release bwa-0.4.4 + +------------------------------------------------------------------------ +r813 | lh3 | 2009-02-15 10:22:50 -0500 (Sun, 15 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.3-5 + * impose boundary check in refine_gapped + +------------------------------------------------------------------------ +r811 | lh3 | 2009-02-14 09:46:13 -0500 (Sat, 14 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.3-4 + * change MD tag to match the latest SAM specification + +------------------------------------------------------------------------ +r810 | lh3 | 2009-02-13 04:46:04 -0500 (Fri, 13 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + +update ChangeLog + +------------------------------------------------------------------------ +r799 | lh3 | 2009-02-05 12:01:17 -0500 (Thu, 05 Feb 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + +change MD tag to meet the latest SAM specification + +------------------------------------------------------------------------ +r796 | lh3 | 2009-02-05 08:35:13 -0500 (Thu, 05 Feb 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.3-2 + * fixed a bug on counting 'N' + +------------------------------------------------------------------------ +r795 | lh3 | 2009-02-05 07:41:27 -0500 (Thu, 05 Feb 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.4.3-1 + * fixed potential boundary problems + * update benchmark result + +------------------------------------------------------------------------ +r791 | lh3 | 2009-01-25 05:20:47 -0500 (Sun, 25 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update some numbers + +------------------------------------------------------------------------ +r790 | lh3 | 2009-01-24 15:13:03 -0500 (Sat, 24 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update benchmark + +------------------------------------------------------------------------ +r789 | lh3 | 2009-01-22 10:18:44 -0500 (Thu, 22 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtindex.c + +a warning message for index + +------------------------------------------------------------------------ +r788 | lh3 | 2009-01-22 09:54:06 -0500 (Thu, 22 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/main.c + +forget to change release number + +------------------------------------------------------------------------ +r786 | lh3 | 2009-01-22 06:27:39 -0500 (Thu, 22 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + +Release bwa-0.4.3 + +------------------------------------------------------------------------ +r785 | lh3 | 2009-01-22 06:27:16 -0500 (Thu, 22 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + +Release bwa-0.4.3 + +------------------------------------------------------------------------ +r784 | lh3 | 2009-01-22 06:19:59 -0500 (Thu, 22 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-10 + * update documentation + * fixed a bug on generating MD tags for SW alignment + +------------------------------------------------------------------------ +r782 | lh3 | 2009-01-19 12:08:38 -0500 (Mon, 19 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-9 + * fixed a bug in samse -n... + +------------------------------------------------------------------------ +r781 | lh3 | 2009-01-19 11:26:37 -0500 (Mon, 19 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-8 + * given -N, the previous version would stop if the top hit is a repeat. Now changed. + +------------------------------------------------------------------------ +r780 | lh3 | 2009-01-19 11:20:18 -0500 (Mon, 19 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-7 + * use a bit-wise flag to replace some member variables in the option struct + * allow to switch off the iterative strategy + +------------------------------------------------------------------------ +r779 | lh3 | 2009-01-19 10:45:57 -0500 (Mon, 19 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-6 + * allow to dump multiple hits from samse, in another format, though + +------------------------------------------------------------------------ +r778 | lh3 | 2009-01-19 06:24:29 -0500 (Mon, 19 Jan 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/kseq.h + A /branches/prog/bwa/kstring.c + A /branches/prog/bwa/kstring.h + M /branches/prog/bwa/main.c + M /branches/prog/bwa/simple_dp.c + + * bwa-0.4.2-5 + * update kseq.h to the latest version + * generate MD tag + * print mate coordinate if only one end is unmapped + +------------------------------------------------------------------------ +r775 | lh3 | 2009-01-18 05:40:35 -0500 (Sun, 18 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-4 + * fixed a bug for SAM format + +------------------------------------------------------------------------ +r774 | lh3 | 2009-01-17 13:48:52 -0500 (Sat, 17 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-3 + * change default fnr to 0.04 + * print max_diff for valid fnr + +------------------------------------------------------------------------ +r773 | lh3 | 2009-01-17 05:54:37 -0500 (Sat, 17 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.4.2-2 + * automatically choose max_diff + +------------------------------------------------------------------------ +r772 | lh3 | 2009-01-16 18:16:14 -0500 (Fri, 16 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.4.2-1 + * take N as a mismatch + +------------------------------------------------------------------------ +r768 | lh3 | 2009-01-09 11:57:23 -0500 (Fri, 09 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/main.c + +Release bwa-0.4.2 + +------------------------------------------------------------------------ +r759 | lh3 | 2009-01-07 09:55:43 -0500 (Wed, 07 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + +Release bwa-0.4.1 + +------------------------------------------------------------------------ +r758 | lh3 | 2009-01-07 05:36:06 -0500 (Wed, 07 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.4.0-2 + * make mate_sw fully working + +------------------------------------------------------------------------ +r757 | lh3 | 2009-01-06 18:04:29 -0500 (Tue, 06 Jan 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.4.0-1 + * do SW alignment for unmapped mate. It is working. + * I still need to do some extra work for SW alignment, but it is too late + and I am getting tired... I will do tomorrow. + +------------------------------------------------------------------------ +r755 | lh3 | 2009-01-06 10:23:29 -0500 (Tue, 06 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.4.0 + +------------------------------------------------------------------------ +r754 | lh3 | 2009-01-06 07:45:02 -0500 (Tue, 06 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtgap.h + M /branches/prog/bwa/main.c + + * bwa-0.3.0-12 + * better lock + +------------------------------------------------------------------------ +r753 | lh3 | 2009-01-06 06:17:21 -0500 (Tue, 06 Jan 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-11 + * fixed a small memory leak in bwa_seq_close() + * fixed "uninitialized memory" from bwt_aln1_t + * multithreading for "aln" command + +------------------------------------------------------------------------ +r752 | lh3 | 2009-01-05 17:34:13 -0500 (Mon, 05 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + D /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwt_gen/bwt_gen.c + A /branches/prog/bwa/bwtmisc.c (from /branches/prog/bwa/pac2bwt.c:748) + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + D /branches/prog/bwa/pac2bwt.c + + * bwa-0.3.0-10 + * a little bit code clean up + +------------------------------------------------------------------------ +r751 | lh3 | 2009-01-05 17:19:04 -0500 (Mon, 05 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-9 + * use 64-bit integer to speed up Occ calculate, although just a little bit + +------------------------------------------------------------------------ +r750 | lh3 | 2009-01-05 16:44:26 -0500 (Mon, 05 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-8 + * a little bit code cleanup + +------------------------------------------------------------------------ +r749 | lh3 | 2009-01-05 16:37:28 -0500 (Mon, 05 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-7 + * accelerate Occ calculation + +------------------------------------------------------------------------ +r748 | lh3 | 2009-01-05 16:12:28 -0500 (Mon, 05 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + M /branches/prog/bwa/pac2bwt.c + + * bwa-0.3.0-6 + * put occ table along with bwt to save another cache miss + * this version is already faster than the previous and I can still improve it... + +------------------------------------------------------------------------ +r747 | lh3 | 2009-01-05 10:16:18 -0500 (Mon, 05 Jan 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-5 + * remove occ_major to save a cache miss; however, OCC_INTERVAL has to be + increased to keep the same memory. As a result, the speed is a little + slower in fact. + +------------------------------------------------------------------------ +r746 | lh3 | 2009-01-05 09:50:53 -0500 (Mon, 05 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-4 + * added back optimization codes (it is a pain...) + +------------------------------------------------------------------------ +r745 | lh3 | 2009-01-05 08:23:00 -0500 (Mon, 05 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-3 + * faster bit operations + +------------------------------------------------------------------------ +r744 | lh3 | 2009-01-05 05:58:46 -0500 (Mon, 05 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-2 + * removed optimization codes again... + * use a new method to count the bits + +------------------------------------------------------------------------ +r743 | lh3 | 2009-01-04 17:18:38 -0500 (Sun, 04 Jan 2009) | 5 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.3.0-1 + * added back the optimization codes + * added a new option to aln: max_entries, although this is disabled by default + * updated benchmark + +------------------------------------------------------------------------ +r742 | lh3 | 2009-01-04 07:56:12 -0500 (Sun, 04 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +add URL + +------------------------------------------------------------------------ +r740 | lh3 | 2009-01-04 07:39:43 -0500 (Sun, 04 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.3.0 + +------------------------------------------------------------------------ +r739 | lh3 | 2009-01-04 06:55:06 -0500 (Sun, 04 Jan 2009) | 2 lines +Changed paths: + A /branches/prog/bwa/COPYING + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bntseq.h + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/utils.c + M /branches/prog/bwa/utils.h + +added licensing information + +------------------------------------------------------------------------ +r738 | lh3 | 2009-01-04 06:18:25 -0500 (Sun, 04 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-31 + * better mapping quality + * update benchmark + +------------------------------------------------------------------------ +r737 | lh3 | 2009-01-03 16:00:58 -0500 (Sat, 03 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bwa.1 + +update documentation + +------------------------------------------------------------------------ +r736 | lh3 | 2009-01-02 10:26:38 -0500 (Fri, 02 Jan 2009) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update documentation + +------------------------------------------------------------------------ +r735 | lh3 | 2009-01-02 07:10:20 -0500 (Fri, 02 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-30 + * reduce memory a little bit + * update documentation + +------------------------------------------------------------------------ +r734 | lh3 | 2009-01-01 13:45:45 -0500 (Thu, 01 Jan 2009) | 8 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-29 + * sampe: removed -O option; changed default -o to 100000 + * sampe: fixed a bug in calculating paired mapping quality + * aln: added an option to search for suboptimal hits even if the best is a repeat. + This option will make sampe MUCH SLOWER. + * sampe: set isize as zero if mapped to two different chr + * update manual (unfinished) + +------------------------------------------------------------------------ +r733 | lh3 | 2009-01-01 11:01:20 -0500 (Thu, 01 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-28 + * fixed a bug in calculating paired mapping quality + +------------------------------------------------------------------------ +r732 | lh3 | 2009-01-01 09:27:46 -0500 (Thu, 01 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + A /branches/prog/bwa/khash.h (from /branches/prog/sclib/khash/khash.h:675) + M /branches/prog/bwa/main.c + + * bwa-0.2.0-27 + * accelerate sampe by storing visited large intervals + +------------------------------------------------------------------------ +r731 | lh3 | 2009-01-01 06:51:21 -0500 (Thu, 01 Jan 2009) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-26 + * remove the optimation codes + +------------------------------------------------------------------------ +r730 | lh3 | 2009-01-01 06:48:59 -0500 (Thu, 01 Jan 2009) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-25 + * accelerate OCC calculation by ~7%. However, it seems not worth doing + this by complicate the codes. I will change back later. + +------------------------------------------------------------------------ +r729 | lh3 | 2008-12-31 16:43:56 -0500 (Wed, 31 Dec 2008) | 6 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-24 + * change command "sai2sam_pe" to "sampe" + * print usage for sampe command + * in sampe: change default max_occ to 1000 + * fixed a few compiling warnings in bntseq.c + +------------------------------------------------------------------------ +r728 | lh3 | 2008-12-27 07:14:59 -0500 (Sat, 27 Dec 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-22 + * mating information can be printed to SAM + +------------------------------------------------------------------------ +r727 | lh3 | 2008-12-26 18:10:59 -0500 (Fri, 26 Dec 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.2.0-21 + * implement pairing (still UNFINISHED) + * output all reads even if full of N + +------------------------------------------------------------------------ +r726 | lh3 | 2008-12-26 13:31:27 -0500 (Fri, 26 Dec 2008) | 5 lines +Changed paths: + M /branches/prog/bwa/Makefile + A /branches/prog/bwa/bwape.c + M /branches/prog/bwa/bwase.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * bwa-0.2.0-20 + * remove "-t" from aln cmd + * code clean up: move some functions in bwt2fmv.c to other source files + * added sai2sam_pe cmd: *UNFINISHED* + +------------------------------------------------------------------------ +r725 | lh3 | 2008-12-26 07:04:11 -0500 (Fri, 26 Dec 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + A /branches/prog/bwa/bwase.c + A /branches/prog/bwa/bwaseqio.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/kseq.h + A /branches/prog/bwa/ksort.h (from /branches/prog/sclib/ksort/ksort.h:712) + A /branches/prog/bwa/kvec.h (from /branches/prog/sclib/kvec/kvec.h:537) + M /branches/prog/bwa/main.c + + * bwa-0.2.0-19 + * considerable code cleanup; no actual changes + +------------------------------------------------------------------------ +r724 | lh3 | 2008-12-25 11:32:11 -0500 (Thu, 25 Dec 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.2.0-18 + * generate SAM output + +------------------------------------------------------------------------ +r723 | lh3 | 2008-12-25 10:48:31 -0500 (Thu, 25 Dec 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * bwa-0.2.0-17 + * remove bwtsw2 related codes + * separate searching for SA interval from generating alignments + +------------------------------------------------------------------------ +r722 | lh3 | 2008-12-25 08:57:13 -0500 (Thu, 25 Dec 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt2fmv.c + D /branches/prog/bwa/bwt_lite.c + D /branches/prog/bwa/bwt_lite.h + M /branches/prog/bwa/bwtgap.c + D /branches/prog/bwa/bwtsw2.h + D /branches/prog/bwa/bwtsw2_aux.c + D /branches/prog/bwa/bwtsw2_core.c + D /branches/prog/bwa/bwtsw2_main.c + D /branches/prog/bwa/khash.h + D /branches/prog/bwa/ksort.h + D /branches/prog/bwa/kvec.h + M /branches/prog/bwa/main.c + + * added interface to "aln -t" + * remove bwtsw2 related codes + +------------------------------------------------------------------------ +r666 | lh3 | 2008-11-18 18:34:29 -0500 (Tue, 18 Nov 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.2.0-16 + * allow to set max mismatches based on read length, but I do not know + whether this really works + +------------------------------------------------------------------------ +r665 | lh3 | 2008-11-18 08:34:03 -0500 (Tue, 18 Nov 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-15 + * fixed a bug in sequence parser. + +------------------------------------------------------------------------ +r612 | lh3 | 2008-10-28 06:50:53 -0400 (Tue, 28 Oct 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/utils.c + + * bwa-0.2.0-14 + * fixed a bug caused by the change of the FASTA/Q parser + +------------------------------------------------------------------------ +r611 | lh3 | 2008-10-28 06:24:56 -0400 (Tue, 28 Oct 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bntseq.h + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtsw2_core.c + A /branches/prog/bwa/kseq.h + D /branches/prog/bwa/seq.c + D /branches/prog/bwa/seq.h + M /branches/prog/bwa/simple_dp.c + M /branches/prog/bwa/utils.c + M /branches/prog/bwa/utils.h + +replace seq.* with kseq.h + +------------------------------------------------------------------------ +r610 | lh3 | 2008-10-27 13:00:04 -0400 (Mon, 27 Oct 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-13 + * make bwtsw2 output sub-optimal hits. not completed + +------------------------------------------------------------------------ +r609 | lh3 | 2008-10-24 16:52:00 -0400 (Fri, 24 Oct 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/kvec.h + +little... + +------------------------------------------------------------------------ +r532 | lh3 | 2008-09-19 05:28:45 -0400 (Fri, 19 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/khash.h + +improve interface of khash + +------------------------------------------------------------------------ +r531 | lh3 | 2008-09-18 06:52:59 -0400 (Thu, 18 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +improve minor things, which make bwtsw2 slower, but should miss less true hits + +------------------------------------------------------------------------ +r530 | lh3 | 2008-09-17 18:19:26 -0400 (Wed, 17 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + + * fixed a bug in calculating ->D + * enforce band-width checking + +------------------------------------------------------------------------ +r529 | lh3 | 2008-09-17 18:06:49 -0400 (Wed, 17 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +delete a line of code that is never visited + +------------------------------------------------------------------------ +r528 | lh3 | 2008-09-17 17:58:51 -0400 (Wed, 17 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +a bit code clean up + +------------------------------------------------------------------------ +r527 | lh3 | 2008-09-17 10:55:45 -0400 (Wed, 17 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-12 + * max-depth can be set, although it does not help the speed at all + +------------------------------------------------------------------------ +r526 | lh3 | 2008-09-16 17:59:36 -0400 (Tue, 16 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +cut_tail after remove duplicate + +------------------------------------------------------------------------ +r525 | lh3 | 2008-09-16 17:56:11 -0400 (Tue, 16 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/khash.h + M /branches/prog/bwa/main.c + + * bwa-0.2.0-11 + * improved cut_tail() + +------------------------------------------------------------------------ +r524 | lh3 | 2008-09-15 16:53:22 -0400 (Mon, 15 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-10 + * fixed a bug in cut_tail() + +------------------------------------------------------------------------ +r518 | lh3 | 2008-09-15 04:35:59 -0400 (Mon, 15 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +a bit code clean up + +------------------------------------------------------------------------ +r517 | lh3 | 2008-09-14 18:18:11 -0400 (Sun, 14 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +improve speed (<1%) + +------------------------------------------------------------------------ +r516 | lh3 | 2008-09-14 18:08:55 -0400 (Sun, 14 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + + * fixed two potential bugs, although I have not seen their effects + * improve speed a bit (<2%) + +------------------------------------------------------------------------ +r515 | lh3 | 2008-09-14 17:26:49 -0400 (Sun, 14 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + +nothing, really + +------------------------------------------------------------------------ +r514 | lh3 | 2008-09-14 17:10:13 -0400 (Sun, 14 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +disable X-drop, which has to be reimplemented in the current algorithm + +------------------------------------------------------------------------ +r513 | lh3 | 2008-09-14 16:49:42 -0400 (Sun, 14 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt_lite.c + M /branches/prog/bwa/bwt_lite.h + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + + * temporarily disable cut_tail() + * calculate SA in bwt_lite.c + * fixed a bug in reversing the sequence + +------------------------------------------------------------------------ +r512 | lh3 | 2008-09-13 17:35:40 -0400 (Sat, 13 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + A /branches/prog/bwa/ksort.h + +n-best method + +------------------------------------------------------------------------ +r507 | lh3 | 2008-09-13 09:06:54 -0400 (Sat, 13 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtsw2_core.c + +give correct result again + +------------------------------------------------------------------------ +r506 | lh3 | 2008-09-13 08:12:07 -0400 (Sat, 13 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +I think I know the reason. It needs more work... + +------------------------------------------------------------------------ +r505 | lh3 | 2008-09-13 06:20:43 -0400 (Sat, 13 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtsw2_core.c + +fixed another bug, but still have + +------------------------------------------------------------------------ +r504 | lh3 | 2008-09-12 18:13:37 -0400 (Fri, 12 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +fixed another bug + +------------------------------------------------------------------------ +r503 | lh3 | 2008-09-12 17:15:56 -0400 (Fri, 12 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/khash.h + + * do not segfault, but the result is WRONG! + * prepare to remove bsw2_connectivity_check() + +------------------------------------------------------------------------ +r502 | lh3 | 2008-09-12 15:52:41 -0400 (Fri, 12 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/kvec.h + +more revisions + +------------------------------------------------------------------------ +r501 | lh3 | 2008-09-11 18:06:15 -0400 (Thu, 11 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +further simply codes with kvec.h + +------------------------------------------------------------------------ +r500 | lh3 | 2008-09-11 17:42:15 -0400 (Thu, 11 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +part of revisions... have not finished + +------------------------------------------------------------------------ +r499 | lh3 | 2008-09-11 17:24:15 -0400 (Thu, 11 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/khash.h + A /branches/prog/bwa/kvec.h + +prepare for abrupt change + +------------------------------------------------------------------------ +r496 | lh3 | 2008-09-11 10:34:38 -0400 (Thu, 11 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +fixed a bug; now "bwtsw2 -d" is useless + +------------------------------------------------------------------------ +r495 | lh3 | 2008-09-11 09:22:03 -0400 (Thu, 11 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/simple_dp.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + +improve speed a little bit + +------------------------------------------------------------------------ +r494 | lh3 | 2008-09-11 08:28:08 -0400 (Thu, 11 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +remove debug codes + +------------------------------------------------------------------------ +r493 | lh3 | 2008-09-11 07:49:53 -0400 (Thu, 11 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + + * improve the speed a little bit (<5%) + * prepare to remove BSW_DEBUG + +------------------------------------------------------------------------ +r492 | lh3 | 2008-09-11 06:15:56 -0400 (Thu, 11 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-9 + * support reverse strand + * fixed a bug that causes missing hits + +------------------------------------------------------------------------ +r491 | lh3 | 2008-09-11 05:46:16 -0400 (Thu, 11 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-8 + * better progress report + +------------------------------------------------------------------------ +r490 | lh3 | 2008-09-10 17:04:49 -0400 (Wed, 10 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-7 + * avoid some missing hits + * add maximum depth + +------------------------------------------------------------------------ +r489 | lh3 | 2008-09-10 11:51:13 -0400 (Wed, 10 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-6 + * bwtsw2 works although on the forward strand only for now + * better progress information + +------------------------------------------------------------------------ +r488 | lh3 | 2008-09-10 10:21:53 -0400 (Wed, 10 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + + * implement memory pool + * avoid some rehashing + +------------------------------------------------------------------------ +r487 | lh3 | 2008-09-10 09:23:38 -0400 (Wed, 10 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_main.c + + * fixed a memory leak + * prepare to implement mempool + +------------------------------------------------------------------------ +r486 | lh3 | 2008-09-10 09:10:09 -0400 (Wed, 10 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/khash.h + + * add X-dropoff + * remove duplicated results + * switch to simple stack + +------------------------------------------------------------------------ +r485 | lh3 | 2008-09-10 06:31:20 -0400 (Wed, 10 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + + * check whether t-node has been visited + * prepare to remove two-level stack + +------------------------------------------------------------------------ +r484 | lh3 | 2008-09-10 05:00:57 -0400 (Wed, 10 Sep 2008) | 2 lines +Changed paths: + A /branches/prog/bwa/khash.h + +khash library + +------------------------------------------------------------------------ +r483 | lh3 | 2008-09-10 04:22:53 -0400 (Wed, 10 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +add inline + +------------------------------------------------------------------------ +r482 | lh3 | 2008-09-09 16:34:57 -0400 (Tue, 09 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + +improve speed + +------------------------------------------------------------------------ +r481 | lh3 | 2008-09-09 13:13:00 -0400 (Tue, 09 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtsw2_core.c + +Use a 128bit hash table to keep all (tk,tl,qk,ql). This is slow. Just +keep a copy in case I may need this in future. + + +------------------------------------------------------------------------ +r480 | lh3 | 2008-09-09 12:53:32 -0400 (Tue, 09 Sep 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_core.c + + * no principal modification + +------------------------------------------------------------------------ +r479 | lh3 | 2008-09-09 11:01:45 -0400 (Tue, 09 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtsw2_core.c + + * fixed a bug which may cause duplicated matching + * accelerate the speed a bit, although using hash in avoiding duplications + slows the speed down in the end + +------------------------------------------------------------------------ +r474 | lh3 | 2008-09-03 17:22:57 -0400 (Wed, 03 Sep 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtsw2.h + M /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-5 + * indel seems to work on toy example + * add band + +------------------------------------------------------------------------ +r469 | lh3 | 2008-09-01 09:18:45 -0400 (Mon, 01 Sep 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt_lite.c + M /branches/prog/bwa/bwt_lite.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtsw2.h + A /branches/prog/bwa/bwtsw2_aux.c + M /branches/prog/bwa/bwtsw2_core.c + M /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/is.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + M /branches/prog/bwa/simple_dp.c + + * bwa-0.2.0-4 + * updated bwtsw2, which seems to work properly on toy examples + +------------------------------------------------------------------------ +r447 | lh3 | 2008-08-27 10:05:09 -0400 (Wed, 27 Aug 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-3 + * tune for longer gaps, but it does not really work with kilo-bp gaps... + +------------------------------------------------------------------------ +r446 | lh3 | 2008-08-26 13:30:41 -0400 (Tue, 26 Aug 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-2 + * changed the way to extend long deletions. Now use max_del_occ. + +------------------------------------------------------------------------ +r445 | lh3 | 2008-08-26 13:05:58 -0400 (Tue, 26 Aug 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt_lite.c + M /branches/prog/bwa/bwt_lite.h + +updated from bwtsw2_lite + +------------------------------------------------------------------------ +r436 | lh3 | 2008-08-23 12:28:44 -0400 (Sat, 23 Aug 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.h + A /branches/prog/bwa/bwt_lite.c + A /branches/prog/bwa/bwt_lite.h + A /branches/prog/bwa/bwtsw2.h + A /branches/prog/bwa/bwtsw2_core.c + A /branches/prog/bwa/bwtsw2_main.c + M /branches/prog/bwa/main.c + + * bwa-0.2.0-1 + * add bwt_lite: a light-weighted version of bwt (NOT TESTED!) + * add core codes for bwtsw2: NOT TESTED!!! + +------------------------------------------------------------------------ +r427 | lh3 | 2008-08-15 05:38:12 -0400 (Fri, 15 Aug 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + +Release bwa-0.2.0 + +------------------------------------------------------------------------ +r426 | lh3 | 2008-08-14 11:26:19 -0400 (Thu, 14 Aug 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + + * bwa-0.1.6-7 + * change default seed length to 31 + * add incomplete support to color sequences (not tested yet!) + +------------------------------------------------------------------------ +r425 | lh3 | 2008-08-14 06:23:11 -0400 (Thu, 14 Aug 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.1.6-6 + * change default seed length to 33bp + +------------------------------------------------------------------------ +r424 | lh3 | 2008-08-14 05:55:33 -0400 (Thu, 14 Aug 2008) | 6 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.1.6-5 + * fixed a bug that may miss true alignments. this bugs exists in most + early versions. + * fixed a bug that yields wrong coordinates for reads mapped on the forward + strands with gaps. + +------------------------------------------------------------------------ +r423 | lh3 | 2008-08-14 04:07:28 -0400 (Thu, 14 Aug 2008) | 2 lines +Changed paths: + D /branches/prog/bwa/Makefile.div + +useless + +------------------------------------------------------------------------ +r422 | lh3 | 2008-08-13 19:21:14 -0400 (Wed, 13 Aug 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.1.6-4 + * fixed one bug + * there is another one... + +------------------------------------------------------------------------ +r421 | lh3 | 2008-08-13 18:23:33 -0400 (Wed, 13 Aug 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtgap.h + M /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/main.c + + * bwa-0.1.6-3 + * almost there, but not quite right + +------------------------------------------------------------------------ +r419 | lh3 | 2008-08-13 17:27:02 -0400 (Wed, 13 Aug 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtgap.h + M /branches/prog/bwa/main.c + + * improve the seeding method + * prepare to load two BWTs into memory. A BIG change! + +------------------------------------------------------------------------ +r418 | lh3 | 2008-08-13 10:56:54 -0400 (Wed, 13 Aug 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtgap.h + M /branches/prog/bwa/main.c + + * added seeding + * unfinished yet + +------------------------------------------------------------------------ +r413 | lh3 | 2008-08-08 11:48:35 -0400 (Fri, 08 Aug 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/main.c + +Release bwa-0.1.6 + +------------------------------------------------------------------------ +r410 | lh3 | 2008-08-06 15:48:22 -0400 (Wed, 06 Aug 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/simple_dp.c + +sw: output alignment score + +------------------------------------------------------------------------ +r407 | lh3 | 2008-08-04 10:01:20 -0400 (Mon, 04 Aug 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + A /branches/prog/bwa/simple_dp.c + M /branches/prog/bwa/stdaln.c + M /branches/prog/bwa/stdaln.h + + * bwa-0.1.5-3 + * added a simple interface to SW/NW alignment + * stdaln-0.9.8 (see header for more details) + +------------------------------------------------------------------------ +r406 | lh3 | 2008-08-01 19:21:59 -0400 (Fri, 01 Aug 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + A /branches/prog/bwa/stdaln.c + A /branches/prog/bwa/stdaln.h + + * bwa-0.1.5-2 + * give accurate gap positions + +------------------------------------------------------------------------ +r405 | lh3 | 2008-08-01 19:06:19 -0400 (Fri, 01 Aug 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + +unfinished, but I am tired... + +------------------------------------------------------------------------ +r401 | lh3 | 2008-07-30 05:59:24 -0400 (Wed, 30 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/main.c + + * bwa-0.1.5-1 + * fixed a potential bug which may produce an alignment in N regions, + although extremely rare. + +------------------------------------------------------------------------ +r399 | lh3 | 2008-07-27 11:41:52 -0400 (Sun, 27 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/main.c + +Release bwa-0.1.5 + +------------------------------------------------------------------------ +r398 | lh3 | 2008-07-25 12:14:47 -0400 (Fri, 25 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update documentation + +------------------------------------------------------------------------ +r397 | lh3 | 2008-07-25 09:58:56 -0400 (Fri, 25 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * + +------------------------------------------------------------------------ +r396 | lh3 | 2008-07-25 06:42:01 -0400 (Fri, 25 Jul 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.1.4-4 + * add timer for debugging + +------------------------------------------------------------------------ +r395 | lh3 | 2008-07-24 05:46:21 -0400 (Thu, 24 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.1.4-3 + * fixed a bug in the previous code + * this version gives identical result to bwa-0.1.4, just 10% faster + +------------------------------------------------------------------------ +r394 | lh3 | 2008-07-24 05:18:53 -0400 (Thu, 24 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtgap.h + M /branches/prog/bwa/main.c + + * bwa-0.1.4-2 + * further improve the speed + * The result is slightly different from bwa-0.1.4 now. I need to check... + +------------------------------------------------------------------------ +r393 | lh3 | 2008-07-23 12:04:16 -0400 (Wed, 23 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt.c + +comments only + +------------------------------------------------------------------------ +r392 | lh3 | 2008-07-23 10:34:03 -0400 (Wed, 23 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + +further improve the speed in Occ functions + +------------------------------------------------------------------------ +r386 | lh3 | 2008-07-22 10:03:54 -0400 (Tue, 22 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/main.c + +Release bwa-0.1.4 + +------------------------------------------------------------------------ +r385 | lh3 | 2008-07-22 09:44:50 -0400 (Tue, 22 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bwa.1 + +update documentation and ChangeLog + +------------------------------------------------------------------------ +r384 | lh3 | 2008-07-22 08:50:03 -0400 (Tue, 22 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.1.3-2 + * fixed the bug in the last modification + * now the alignment should be more clearly defined + +------------------------------------------------------------------------ +r383 | lh3 | 2008-07-21 18:32:21 -0400 (Mon, 21 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.1.3-1 + * this is a buggy verion! + * i will fix the bug tomorrow. It is late... + +------------------------------------------------------------------------ +r381 | lh3 | 2008-07-21 06:45:32 -0400 (Mon, 21 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.1.3 + +------------------------------------------------------------------------ +r380 | lh3 | 2008-07-21 06:07:43 -0400 (Mon, 21 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/main.c + + * bwa-0.1.2-3 + * improve the speed for gcc on Intel Mac OS X, but not really on icc on Linux + * aln: more command-line options + +------------------------------------------------------------------------ +r373 | lh3 | 2008-07-17 09:09:46 -0400 (Thu, 17 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/main.c + + * bwa-0.1.2-2 + * further improve the speed + * this version gives exactly the same result as bwa-0.1.2 + +------------------------------------------------------------------------ +r372 | lh3 | 2008-07-17 07:51:08 -0400 (Thu, 17 Jul 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/main.c + + * bwa-0.1.2-1 + * speed up by about 5% + +------------------------------------------------------------------------ +r370 | lh3 | 2008-07-17 05:12:00 -0400 (Thu, 17 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.1.2 + +------------------------------------------------------------------------ +r368 | lh3 | 2008-07-16 08:51:25 -0400 (Wed, 16 Jul 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + D /branches/prog/bwa/bwt1away.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtgap.h + D /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.1-9 + * some code cleanup + * remove 1away and top2 + +------------------------------------------------------------------------ +r367 | lh3 | 2008-07-16 08:24:34 -0400 (Wed, 16 Jul 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/is.c + +Yuta Mori's implementation of IS algorithm. + +------------------------------------------------------------------------ +r365 | lh3 | 2008-07-16 06:58:04 -0400 (Wed, 16 Jul 2008) | 6 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwtgap.h + M /branches/prog/bwa/main.c + + * bwa-0.1.1-8 + * improve gapped alignment + * this version will miss more gapped alignments, but the speed is much faster + * prepare to remove top2 and 1away algorithms + * prepare to add SAIS algorithm for bwt construction + +------------------------------------------------------------------------ +r358 | lh3 | 2008-06-09 06:03:04 -0400 (Mon, 09 Jun 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.1.1-7 + * change END_SKIP from 3 to 5, but still gaps may be wrongly added + * change default '-g' from 5 to 3 + +------------------------------------------------------------------------ +r357 | lh3 | 2008-06-09 05:18:36 -0400 (Mon, 09 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.1.1-6 + * fix a bug in nested stack + +------------------------------------------------------------------------ +r356 | lh3 | 2008-06-08 18:43:13 -0400 (Sun, 08 Jun 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + A /branches/prog/bwa/bwtgap.h + M /branches/prog/bwa/main.c + + * bwa-0.1.1-5 + * replace heap with nested stacks + * there are still obvious bugs... + +------------------------------------------------------------------------ +r355 | lh3 | 2008-06-08 17:13:44 -0400 (Sun, 08 Jun 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * bwa-0.1.1-4 + * add interface to affine gap alignment + * there are obvious bugs and I will fix them later + +------------------------------------------------------------------------ +r354 | lh3 | 2008-06-08 15:39:05 -0400 (Sun, 08 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/main.c + + * bwa-0.1.1-3 + * affine gap seems to work, at least partially + +------------------------------------------------------------------------ +r353 | lh3 | 2008-06-08 09:27:18 -0400 (Sun, 08 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + A /branches/prog/bwa/bwtgap.c + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.1-2 + * initial gapped alignment. not work at the moment + +------------------------------------------------------------------------ +r352 | lh3 | 2008-06-06 04:37:34 -0400 (Fri, 06 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.1-1 + * ungap: remove a useless varible in top2_entry_t + +------------------------------------------------------------------------ +r348 | lh3 | 2008-06-03 09:04:12 -0400 (Tue, 03 Jun 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/ChangeLog + A /branches/prog/bwa/NEWS + M /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/main.c + +Release bwa-0.1.1 + +------------------------------------------------------------------------ +r347 | lh3 | 2008-06-03 05:45:08 -0400 (Tue, 03 Jun 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwa.1 + +update documentation + +------------------------------------------------------------------------ +r346 | lh3 | 2008-06-02 18:59:50 -0400 (Mon, 02 Jun 2008) | 5 lines +Changed paths: + A /branches/prog/bwa/ChangeLog + A /branches/prog/bwa/bwa.1 + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-11 + * improve approximating mapping qualities + * add documentation + * add ChangeLog + +------------------------------------------------------------------------ +r345 | lh3 | 2008-06-02 16:04:39 -0400 (Mon, 02 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-10 + * output a random position for repetitive reads + +------------------------------------------------------------------------ +r344 | lh3 | 2008-06-02 15:03:54 -0400 (Mon, 02 Jun 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/pac2bwt.c + + * bwa-0.1.0-9 + * fix memory leaks + * fix a potential bug in coverting to the real coordinate + +------------------------------------------------------------------------ +r343 | lh3 | 2008-06-02 13:44:51 -0400 (Mon, 02 Jun 2008) | 5 lines +Changed paths: + M /branches/prog/bwa/Makefile.div + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-8 + * fix a bug about strand + * update Makefile.div + * change top2b as the default method + +------------------------------------------------------------------------ +r342 | lh3 | 2008-06-02 11:23:26 -0400 (Mon, 02 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt1away.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-7 + * use bwt_2occ() and bwt_2occ4() in other functions + +------------------------------------------------------------------------ +r341 | lh3 | 2008-06-02 09:31:39 -0400 (Mon, 02 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-6 + * fix a bug for missing hits + +------------------------------------------------------------------------ +r340 | lh3 | 2008-06-02 09:10:18 -0400 (Mon, 02 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-5 + * accelerate comparisons in heap, a bit + +------------------------------------------------------------------------ +r339 | lh3 | 2008-06-02 08:41:31 -0400 (Mon, 02 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-4 + * avoid marginal repeated calculation in occ + +------------------------------------------------------------------------ +r338 | lh3 | 2008-06-02 06:46:51 -0400 (Mon, 02 Jun 2008) | 5 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-3 + * fix a bug caused by previours change + * fix a bug in heap + * order the heap by more criteria + +------------------------------------------------------------------------ +r337 | lh3 | 2008-06-01 19:11:15 -0400 (Sun, 01 Jun 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + + * bwa-0.1.0-2 + * also sort sa range in heapsort, in attempt to improve cache performance. + Unfortunately, it does not work well at all. + +------------------------------------------------------------------------ +r336 | lh3 | 2008-06-01 17:45:23 -0400 (Sun, 01 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/Makefile.div + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/main.c + + * 0.1.0-1 + * fix a bug in calculating the real coordinate + +------------------------------------------------------------------------ +r335 | lh3 | 2008-06-01 16:03:09 -0400 (Sun, 01 Jun 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + +nothing, really + +------------------------------------------------------------------------ +r334 | lh3 | 2008-06-01 15:59:13 -0400 (Sun, 01 Jun 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + A /branches/prog/bwa/Makefile.div + M /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/pac2bwt.c + +use IS algorithm by default + +------------------------------------------------------------------------ +r333 | lh3 | 2008-06-01 15:05:15 -0400 (Sun, 01 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/is.c + M /branches/prog/bwa/pac2bwt.c + + * a bit code clean up in is.c + * add IS algorithm for constructing BWT, albeit slower + +------------------------------------------------------------------------ +r332 | lh3 | 2008-06-01 13:23:08 -0400 (Sun, 01 Jun 2008) | 2 lines +Changed paths: + A /branches/prog/bwa/is.c + +IS linear-time algorithm for constructing SA/BWT + +------------------------------------------------------------------------ +r331 | lh3 | 2008-06-01 10:35:26 -0400 (Sun, 01 Jun 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bntseq.c + A /branches/prog/bwa/bwtindex.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * fix a bug in generating .pac + * index in one go + +------------------------------------------------------------------------ +r330 | lh3 | 2008-06-01 09:17:05 -0400 (Sun, 01 Jun 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bntseq.h + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwttop2.c + +real coordinates can be ouput + +------------------------------------------------------------------------ +r329 | lh3 | 2008-05-31 19:21:02 -0400 (Sat, 31 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwttop2.c + +add top2e which is similar to 1away + +------------------------------------------------------------------------ +r328 | lh3 | 2008-05-31 18:46:12 -0400 (Sat, 31 May 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwttop2.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * unified cmd-line interface for ungapped alignment + * add two alternatives to top2 algorithm + +------------------------------------------------------------------------ +r327 | lh3 | 2008-05-31 18:14:46 -0400 (Sat, 31 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + +add cmd-line interface to alntop2 + +------------------------------------------------------------------------ +r326 | lh3 | 2008-05-31 17:59:31 -0400 (Sat, 31 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt1away.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + A /branches/prog/bwa/bwttop2.c + +top2 algorithm seems to work. I need to change interface, though + +------------------------------------------------------------------------ +r325 | lh3 | 2008-05-31 15:11:49 -0400 (Sat, 31 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt1away.c + +change the variable in the structure + +------------------------------------------------------------------------ +r324 | lh3 | 2008-05-31 14:52:13 -0400 (Sat, 31 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt1away.c + +set a slightly better bound on the maximum allowed mismatches + +------------------------------------------------------------------------ +r323 | lh3 | 2008-05-30 18:40:21 -0400 (Fri, 30 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + + * output time statistics + +------------------------------------------------------------------------ +r322 | lh3 | 2008-05-30 17:58:25 -0400 (Fri, 30 May 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + A /branches/prog/bwa/bwt1away.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + + * presumably better way to make use of prefix. But for the moment I do + not know whether it is correct or not. + * a bit code clean up: separate alignment part + +------------------------------------------------------------------------ +r321 | lh3 | 2008-05-30 13:57:43 -0400 (Fri, 30 May 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt_gen/Makefile + M /branches/prog/bwa/bwt_gen/bwt_gen.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + M /branches/prog/bwa/pac2bwt.c + + * a bit code clean up + * put bwt_gen in bwa + +------------------------------------------------------------------------ +r320 | lh3 | 2008-05-30 11:40:11 -0400 (Fri, 30 May 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtio.c + + * improve cmd-line interface + * fix a bug in loading .sa + * change default sa interval to 32 + +------------------------------------------------------------------------ +r319 | lh3 | 2008-05-30 10:31:37 -0400 (Fri, 30 May 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwtaln.c + + * fix memory leak (I know that. Just a bit lazy) + * change to another method to do 1-away alignment + +------------------------------------------------------------------------ +r318 | lh3 | 2008-05-30 09:21:49 -0400 (Fri, 30 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + +best unique match is partially finished + +------------------------------------------------------------------------ +r317 | lh3 | 2008-05-30 06:33:28 -0400 (Fri, 30 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + +remove "ungapped" command and related codes + +------------------------------------------------------------------------ +r316 | lh3 | 2008-05-30 06:05:20 -0400 (Fri, 30 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + +change variable name thick to width + +------------------------------------------------------------------------ +r315 | lh3 | 2008-05-29 19:06:13 -0400 (Thu, 29 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + M /branches/prog/bwa/pac2bwt.c + +revised algorithm for ungapped alignment. the old one can still be used. + +------------------------------------------------------------------------ +r314 | lh3 | 2008-05-29 16:36:11 -0400 (Thu, 29 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwt_gen/bwt_gen.c + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/pac2bwt.c + + * make commands more independent, but ungapped does not work at the moment + +------------------------------------------------------------------------ +r313 | lh3 | 2008-05-29 15:56:14 -0400 (Thu, 29 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt_gen/bwt_gen.c + +little... + +------------------------------------------------------------------------ +r312 | lh3 | 2008-05-29 15:54:01 -0400 (Thu, 29 May 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt_gen/bwt_gen.c + M /branches/prog/bwa/bwt_gen/bwt_gen.h + + * add CopyRight information from the original codes + * do not dump .fmv files + +------------------------------------------------------------------------ +r311 | lh3 | 2008-05-29 15:44:36 -0400 (Thu, 29 May 2008) | 2 lines +Changed paths: + A /branches/prog/bwa/bwt_gen + A /branches/prog/bwa/bwt_gen/Makefile + A /branches/prog/bwa/bwt_gen/QSufSort.c + A /branches/prog/bwa/bwt_gen/QSufSort.h + A /branches/prog/bwa/bwt_gen/bwt_gen.c + A /branches/prog/bwa/bwt_gen/bwt_gen.h + +codes from BWT-SW, for building BWT from packed file + +------------------------------------------------------------------------ +r310 | lh3 | 2008-05-28 17:03:35 -0400 (Wed, 28 May 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * change OCC_INTERVAL to 0x40, which makes bwa twice as fast. + * write Occ file as ".occ" as it is using a different interval from + .fmv, the BWT-SW correspondance of .occ + +------------------------------------------------------------------------ +r309 | lh3 | 2008-05-28 11:39:37 -0400 (Wed, 28 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt2fmv.c + +fix a bug + +------------------------------------------------------------------------ +r308 | lh3 | 2008-05-28 09:56:16 -0400 (Wed, 28 May 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt2fmv.c + +add heuristics to improve the speed, but I have not tested whether the +results are correct or not. + + +------------------------------------------------------------------------ +r307 | lh3 | 2008-05-28 06:31:34 -0400 (Wed, 28 May 2008) | 5 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/bwtaln.c + M /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * make ungapped alignment basically works... + * but it is very slow in comparison to others... + * also I need to improve the interface... + * a lot of things to keep me busy today... + +------------------------------------------------------------------------ +r306 | lh3 | 2008-05-27 18:41:27 -0400 (Tue, 27 May 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwtaln.c + + * remove recursion + * fixed a bug in bwt_occ() + +------------------------------------------------------------------------ +r305 | lh3 | 2008-05-27 16:59:44 -0400 (Tue, 27 May 2008) | 5 lines +Changed paths: + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwtaln.c + + * bwa now tells whether a sequenced can be mapped with maximum allowed + mismatches. ONLY ungapped. + * this is a recursive version. I will remove recursion later. + + +------------------------------------------------------------------------ +r304 | lh3 | 2008-05-27 09:12:17 -0400 (Tue, 27 May 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + A /branches/prog/bwa/bwtaln.c + A /branches/prog/bwa/bwtaln.h + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + M /branches/prog/bwa/utils.c + + * load .sa and .fmv files + * exact alignment now works + +------------------------------------------------------------------------ +r303 | lh3 | 2008-05-27 06:33:38 -0400 (Tue, 27 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/utils.c + M /branches/prog/bwa/utils.h + +add xassert and fix a bug + +------------------------------------------------------------------------ +r302 | lh3 | 2008-05-27 06:23:20 -0400 (Tue, 27 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwtio.c + A /branches/prog/bwa/utils.c + A /branches/prog/bwa/utils.h + +improve error message and error handling + +------------------------------------------------------------------------ +r301 | lh3 | 2008-05-27 05:37:51 -0400 (Tue, 27 May 2008) | 4 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + A /branches/prog/bwa/bwtio.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + + * move I/O codes to bwtio.c + * SA can be dumped and interestingly, it is identical to BWTSW + * now, .fmv is still different from BWTSW + +------------------------------------------------------------------------ +r299 | lh3 | 2008-05-26 18:07:44 -0400 (Mon, 26 May 2008) | 2 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + +generate/retrieve SA and Occ + +------------------------------------------------------------------------ +r298 | lh3 | 2008-05-26 13:16:49 -0400 (Mon, 26 May 2008) | 3 lines +Changed paths: + M /branches/prog/bwa/bntseq.h + M /branches/prog/bwa/bwt.c + M /branches/prog/bwa/bwt.h + M /branches/prog/bwa/bwt2fmv.c + + * retrieve occ value at any position + * move bwt_cal_occ() to bwt.c + +------------------------------------------------------------------------ +r297 | lh3 | 2008-05-25 17:43:58 -0400 (Sun, 25 May 2008) | 6 lines +Changed paths: + M /branches/prog/bwa/Makefile + A /branches/prog/bwa/bwt.c + A /branches/prog/bwa/bwt.h + A /branches/prog/bwa/bwt2fmv.c + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + M /branches/prog/bwa/pac2bwt.c + + * add bwt2fmv. It works to some extend. However, I do not understand + the purpose of some weird codes in BWT-SW. As a consequence, bwt2fmv + could generate a file almost identical, but not exactly identical, to + the .fmv file from BWT-SW. + + +------------------------------------------------------------------------ +r296 | lh3 | 2008-05-24 18:35:02 -0400 (Sat, 24 May 2008) | 5 lines +Changed paths: + M /branches/prog/bwa/Makefile + M /branches/prog/bwa/bntseq.c + M /branches/prog/bwa/bntseq.h + M /branches/prog/bwa/main.c + M /branches/prog/bwa/main.h + A /branches/prog/bwa/pac2bwt.c + +Burrows-Wheeler Transform now works. At least on one example, the +current code generates the same BWT as BWT-SW. Kind of magical, I would +say. :) + + +------------------------------------------------------------------------ +r295 | lh3 | 2008-05-24 11:25:31 -0400 (Sat, 24 May 2008) | 3 lines +Changed paths: + A /branches/prog/bwa/Makefile + M /branches/prog/bwa/bntseq.c + A /branches/prog/bwa/main.c + A /branches/prog/bwa/main.h + + * add Makefile and main.* + * improve interface to fa2bns, a bit + +------------------------------------------------------------------------ +r293 | lh3 | 2008-05-24 10:57:03 -0400 (Sat, 24 May 2008) | 3 lines +Changed paths: + A /branches/prog/bwa + A /branches/prog/bwa/bntseq.c + A /branches/prog/bwa/bntseq.h + A /branches/prog/bwa/seq.c + A /branches/prog/bwa/seq.h + + * Burrow-Wheeler Alignment + * initial codes + +------------------------------------------------------------------------