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view pyPRADA_1.2/tools/bwa-0.5.7-mh/ChangeLog @ 0:acc2ca1a3ba4
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| author | siyuan |
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| date | Thu, 20 Feb 2014 00:44:58 -0500 |
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------------------------------------------------------------------------ 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 ------------------------------------------------------------------------