zzh
40544d02fe
在gz_read部分加了异步读取
2025-01-13 20:24:20 +08:00
zzh
b50360bb48
整合了ert seeding，结果正确，完善了shm
2024-08-06 03:08:10 +08:00
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
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
d1a5715e56
将fputs改成fwrite，写入效率提升30%
2024-04-06 20:53:42 +08:00
zzh
d41c038616
清理一些fprintf
2024-04-06 16:08:43 +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
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
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
zzh
293f3bb80e
添加了fmt_idx文件，开始改进seed过程
2023-12-25 11:11:19 +08:00
c7c2e6ddf7
Document that the XB tag now contains the mapping quality too
2022-05-19 13:43:22 -04:00
49c397d16e
Merge branch 'feature/add-xa-drop-ratio-option' of https://github.com/fulcrumgenomics/bwa into fulcrumgenomics-feature/add-xa-drop-ratio-option
2022-03-06 18:21:49 -05:00
e679702118
Merge pull request #292 from nh13/patch-1
...
Document "-u"
2022-03-06 18:16:09 -05:00
4d8fb2ca91
Merge pull request #297 from nh13/patch-3
...
Clarify bwa mem -5 option
2022-03-06 18:12:09 -05:00
d422bdbed9
debug flag to measure memory
2021-02-22 23:26:03 -05:00
b58da139c3
Clarify bwa mem -5 option
...
Clarify that the -5 bwa mem option chooses the alignment that starts earliest in the read relative to the read/sequencing order, not genomic coordinate order
2020-08-18 23:01:43 -07:00
34caf50d46
allow the user to specify the XA drop ratio via the -z option
2020-08-12 09:01:44 -07:00
9cbbd6bf94
Update fastmap.c
2020-08-12 08:51:19 -07:00
1a11a6f4b9
Document "-u"
2020-08-06 10:08:29 -07:00
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
47d9fb27d7
Release 0.7.16-r1180
2017-07-30 22:35:38 -04:00
c56c2e4677
Several trivial Debian patches
...
[Andreas Tille]
Check exact number of arguments of bwtupdate
Fix spelling
[Fabian Klötzl]
change printing as size_t is unsigned
2017-07-04 21:24:15 +01:00
bc58bf265d
Add "bwa mem -o FILE" synonym and documentation
...
As -o is still free in the mem command, use that standard option to
specify an output file (and keep -f to parallel bwase/bwape commands).
Document it in the usage and man page.
2017-06-27 17:05:44 +01:00
d28da05f36
Added option to write output to file
2017-06-27 16:47:13 +01:00
f123871451
r1142: added option -5 for Hi-C data
2016-05-31 11:01:36 -04:00
1e6a10ce2d
a typo in fastmap command-line prompt
2016-02-01 11:41:46 -05:00
1247dc2346
removed the pbread mode
...
It is not working well. Not at all.
2016-01-26 22:37:01 -05:00
ed95769a33
updated documentations
...
(prepare for release)
2014-12-21 16:30:29 -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
9bf898fa10
r963: expose mask_level
2014-10-30 11:33:43 -04:00
76a15ea91b
r933: with bwa-postalt ready, drop option -g
2014-10-21 00:23:14 -04:00
zzh
zzh
clintval
Heng Li
Heng Li
Nils Homer
Nils Homer
Andreas Tille
John Marshall
José Manuel Abuín Mosquera