zzh
b50360bb48
整合了ert seeding，结果正确，完善了shm
2024-08-06 03:08:10 +08:00
zzh
9c9502d584
clean代码，结果正确
2024-07-26 04:15:55 +08:00
zzh
8c2a90e3e2
修改了双线程解压读写fastq.gz的bug，修改了一些测试代码
2024-06-24 18:11:54 +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
zzh
dd03596997
加入了获取reads和extension数据的代码
2024-03-27 23:47:39 +08:00
zzh
1e3965cb7d
添加了可同时读写的pipeline，优化了时间统计
2024-03-24 04:40:09 +08:00
zzh
d728ddbe2c
解决了bsw上边界同样的问题，解决了seed3的一个bug
2024-03-23 03:23:05 +08:00
zzh
2eaeb26858
添加了直接扩展两个碱基的函数
2024-03-14 15:32:34 +08:00
zzh
856a0e0c01
改成了batch模式，对na12878有效果
2024-03-09 11:39:40 +08:00
zzh
7d085962a2
开始改成sbwa那种batch模式
2024-03-07 18:23:21 +08:00
6e1dd08fb6
将seed和extend部分修改成了batch模式，好像没啥效果
2024-02-23 01:09:08 +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
17618ee5f2
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
fc2e0d9b0b
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
4a1c2cd3db
修改一些注释疏忽的问题
2024-02-16 21:23:55 +08:00
7dceae8c5d
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
9d45fd02fb
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
5d8ace386f
seed1和seed2结果都正确
2024-02-13 13:37:07 +08:00
d41b8da061
kmer长度变为14，结果正确
2024-02-12 20:54:57 +08:00
463f7da138
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
bf678f4dae
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
c981585fd2
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
f5e83701ab
Add the mate mapping quality tag
2021-07-21 11:12:27 -07:00
ddbd5f7fb7
Removed the debug output; resolves #320
2021-03-09 08:56:52 -05:00
e2dbfe60e3
output more memory information
2021-02-23 10:43:41 -05:00
d422bdbed9
debug flag to measure memory
2021-02-22 23:26:03 -05:00
02a9add042
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
zzh
zzh
Nils Homer
Heng Li
Nils Homer