zzh
364ee9756e
添加了共享内存支持，成功构建ert索引
2024-08-03 17:26:32 +08:00
zzh
123aceb6a6
将fmt和kmer合并到建索引的过程中
2024-04-02 07:49:38 +08:00
zzh
20e072f6af
所有代码都合并了，还差一点建立索引的时候，一起都建立了
2024-04-02 07:42:37 +08:00
4bd0fd4f91
做了一些代码清理，目前结果应该是完全一致的
2024-02-22 01:26:57 +08:00
5b96937edc
deprecate bwasw
2021-03-09 00:52:20 -05:00
94ff6b297a
added the MIT license header to main.c
2020-07-02 13:49:42 -04:00
cd29a7cb54
r1198: exit if .alt is malformatted
...
Resolves #232
2019-01-23 13:28:11 -05:00
11d53b06fb
Merge branch 'dev' into XB
2018-04-02 10:47:45 -04:00
9f26bfcc77
Released bwa-0.7.17 (r1188)
2017-10-23 13:10:17 -04:00
b582816211
r1187: a typo in command line help
2017-09-26 09:35:19 -04:00
340babdd67
r1185: don't lower supp mapq with -5
2017-09-11 09:58:41 -04:00
a9c688ac92
r1181: fixed a segfault ( #145 ) due to ( #138 )
2017-07-31 07:55:35 -04:00
47d9fb27d7
Release 0.7.16-r1180
2017-07-30 22:35:38 -04:00
298284d754
r1144: output debugging message to stderr
2017-06-08 16:06:13 -04:00
f123871451
r1142: added option -5 for Hi-C data
2016-05-31 11:01:36 -04:00
850dd811fc
Release bwa-0.7.15-r1140
2016-05-31 09:42:50 -04:00
58bcc251f2
r1138: fixed typo in insert size estimate ( #65 )
...
credit to @sjackman
2016-05-20 18:05:15 -04:00
5db0c362f5
Release 0.7.14-r1136
2016-05-04 14:41:37 -04:00
7ec3261877
r1134: use AH:* instead of AH:Y
2016-05-03 11:28:58 -04:00
3c038250f9
r1130: changed "ah" to "AH"
2016-04-28 15:39:18 -04:00
9e5852c540
Released bwa-0.7.13 (r1126)
2016-02-23 11:24:19 -05:00
86170ffd2f
r1102: resumed versioning
2016-02-01 11:57:14 -05:00
3ae437ac13
r1044: fixed an out-of-order bug in kthread
2015-03-25 12:16:06 -04:00
163f949a33
added maxk: max unique k-mer at each position
2015-02-08 16:49:25 -05:00
8211fbcb62
Released 0.7.12
2014-12-28 15:44:59 -05:00
e746a3eac7
r1038: wrong 0x100|0x800 flags in PE mode
2014-12-24 13:22:46 -05:00
3ae8d4b80b
r1037: wrong read number flag
2014-12-24 00:55:33 -05:00
b9bbf2d3df
r1036: PE ALT mapping incorrect
...
No SA/XA tags!
2014-12-24 00:49:50 -05:00
408fd5e072
Released bwa-0.7.11-r1034
2014-12-23 15:29:18 -05:00
c561759222
r1027: segfault caused by the last commit
2014-12-12 16:56:54 -05:00
925ddfb697
r1025: accept file with -H; allow to replace @SQ
2014-12-11 10:38:36 -05:00
9d8c906e4c
r1017: process I/O in a separate thread
...
Previously, bwa-mem waits for I/O. When the input data comes from a slow source
(I/O or piped from a slow program), bwa-mem may spend significant amount of
wall-clock time in the single-thread mode. The same may also happen when bwa-mem
writes to slow target. This commit uses two sequence buffers. it allows bwa-mem
to map one buffer while filling or dumping the other buffer. When bwa-mem is run
on 16 threads using the bwa.kit pipeline, the wall clock time is reduced by 30%.
2014-11-26 12:32:48 -05:00
b5f6ed3020
r1005: insert arbitrary header lines
2014-11-19 10:59:05 -05:00
80e4ecfa79
r998: smart pairing; allow mixture of SE/PE reads
2014-11-18 14:30:22 -05:00
c5fe18438a
r984: updated to the latest kseq.h
2014-11-13 11:12:23 -05:00
7eabcf42c4
r983: bugfix - wrong mate info
...
Picard now gives a clean bill.
2014-11-10 13:15:11 -05:00
9bf898fa10
r963: expose mask_level
2014-10-30 11:33:43 -04:00
6db2fd98aa
r960: merge changes from the master branch
2014-10-28 13:46:40 -04:00
3d129be642
r943: change the default -y to 20, but ...
...
for GRCh38 ALT, this is not enough. We need -y at least 40 to get high accuracy
because a locus at chr19 has 35 copies.
2014-10-22 12:42:58 -04:00
4177d6c2c7
r942: ignore ALT hits when counting n_sub for ...
...
non-ALT hits. Counting leads to underestimated mapQ.
2014-10-22 10:24:16 -04:00
60b728487a
r941: set a min length for 3rd-round seeding
2014-10-21 13:15:42 -04:00
282130a64e
r940: fixed a bug - missing primary hit
2014-10-21 12:57:49 -04:00
5e00d08346
r939: fixed a memory leak (issue #35 )
2014-10-21 09:26:19 -04:00
76a15ea91b
r933: with bwa-postalt ready, drop option -g
2014-10-21 00:23:14 -04:00
a6b5a30dab
r930: use 3rd round seeding by default
...
This strategy is similar to the seeding heuristic used by LAST. When it is used
alone, it is not as accurate as the current seeding strategy at least for short
reads. However, it may do a better job for a long contig mapped to multiple ALT
contigs. This seeding strategy is also relatively cheap to perform.
2014-10-20 17:34:15 -04:00
038af2a551
r929: added simplified LAST-like seeding
2014-10-20 17:00:31 -04:00
3370ae9e35
r926: prepare to move -g to bwa-postalt.js
2014-10-19 20:43:53 -04:00
a06646493b
r915: fixed broken example.c
2014-10-17 16:17:28 -04:00
8af17b3478
r912: very minor improvement
2014-10-17 12:14:18 -04:00
c280274331
r911: check before attempting adding
2014-10-17 12:13:09 -04:00
zzh
zzh
Heng Li