198fe34ddb
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
57a6ff7b07
解决了sa的bug，现在结果和原版一模一样
2024-02-21 15:21:56 +08:00
c288e1b285
实现了seed过程的所有加速想法，seed部分实现了3倍左右加速比
2024-02-20 01:12:02 +08:00
95fd6e018b
修改一些注释疏忽的问题
2024-02-16 21:23:55 +08:00
e9022723e6
seed三个步骤，全部用fmt实现，而且结果一致
2024-02-16 20:59:59 +08:00
980588a9ac
添加了bit过滤，解决了一些bug，现在seed1和seed2都没问题了
2024-02-16 00:18:14 +08:00
76c32542e7
seed1和seed2结果都正确
2024-02-13 13:37:07 +08:00
32be32c661
kmer长度变为14，结果正确
2024-02-12 20:54:57 +08:00
44b7c62715
将smem1函数用fmt结构实现了，结果基本正确
2024-02-07 22:08:51 +08:00
zzh
e18e60c0b5
实现了用33bit表示sa，间隔为4，释放内存的时候会崩溃
2023-12-27 10:42:12 +08:00
zzh
ed01396d73
添加了运行时间计算代码，用来分析性能
2023-12-25 13:58:15 +08:00
d8dd308a1f
Add the mate mapping quality tag
2021-07-21 11:12:27 -07:00
34374c5613
Removed the debug output; resolves #320
2021-03-09 08:56:52 -05:00
f1d1fd7c42
output more memory information
2021-02-23 10:43:41 -05:00
b9accf95ad
debug flag to measure memory
2021-02-22 23:26:03 -05:00
436aceb4ef
added MIT license to some non-GPL source files
2020-07-01 23:02:01 -04:00
11d53b06fb
Merge branch 'dev' into XB
2018-04-02 10:47:45 -04:00
eb7dbc1429
optionally write XB to include alignment score
...
request from 4DN-DCIC
2018-04-02 10:43:41 -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
3b96dcee7f
Mem should set the mate cigar tag.
2017-07-03 08:51:00 -07:00
f123871451
r1142: added option -5 for Hi-C data
2016-05-31 11:01:36 -04:00
1247dc2346
removed the pbread mode
...
It is not working well. Not at all.
2016-01-26 22:37:01 -05:00
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
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
76a365a95f
r907: revert to -g.8 by default
2014-10-16 15:56:33 -04:00
d8d8b230d1
r906: don't reduce non-ALT mapQ by default
2014-10-16 15:15:23 -04:00
2a18fa114f
r895: increase the default max_XA_hits_alt to 200
...
Because there are >100 HLA haplotypes
2014-10-14 16:58:42 -04:00
a03d01f944
r878: XA is given to the best alignment
...
Non-ALT hits may get ALT hits in the XA tag. This will simplify haplotype
assignment.
2014-09-30 13:50:51 -04:00
dae4ca3ced
r875: invalid SAM output for ALT hits
2014-09-26 15:29:08 -04:00
7426a750ec
r868: use soft clip for ALT hits
2014-09-19 16:58:18 -04:00
9af36064e8
r867: fixed a few bugs; added ALT hits to XA
2014-09-19 16:50:21 -04:00
a41afe4c97
These files were committed on a wrong branch
2014-09-18 10:49:35 -04:00
c982443210
r854: improved the calculation of pa
...
and build pa filtering into BWA-MEM
2014-09-17 16:26:28 -04:00
825ae92e58
r849: the pa tag now gives a number
...
... which is the ratio of this hit to the best ALT hit.
2014-09-17 13:05:35 -04:00
6f37c14f26
r848: tag alignments with primary ALT
2014-09-16 18:52:49 -04:00
4b6eeb34c8
r830: optionally fixed chunk size
2014-09-15 23:42:24 -04:00
624687b072
r829: killed a harmless gcc warning
2014-09-15 23:33:22 -04:00
b07587f806
r827: an alt hit as good as a pri hit as supp
2014-09-15 16:07:51 -04:00
aee53f1334
r824: ALT mapping seems working
2014-09-15 00:29:05 -04:00
015ab3f6c3
r823: towards ALT support
2014-09-14 16:41:14 -04:00
8116bcc786
Merge branch 'dev' into alt
2014-09-14 15:40:52 -04:00
8d2b93156b
r821: more relax on containing seeds
2014-09-12 10:35:49 -04:00
zzh
zzh
Nils Homer
Heng Li
Nils Homer