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
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[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
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
bfd5e1840f
shm works on small files, but not large ones
...
I don't know why. SHMMAX, SHMALL and SHMMNI are large enough.
2014-10-15 15:44:06 -04:00
0a2cf98293
r876: optionally ignore idxbase.alt file
2014-09-27 23:21:50 -04:00
9af36064e8
r867: fixed a few bugs; added ALT hits to XA
2014-09-19 16:50:21 -04:00
c982443210
r854: improved the calculation of pa
...
and build pa filtering into BWA-MEM
2014-09-17 16:26:28 -04:00
92bc6849a3
r844: added intra-species contig mapping mode
2014-09-16 10:53:07 -04:00
90518f11e3
r843: presetting for ONT 2d reads
...
Somewhat working for 1d reads, but not very well
2014-09-16 10:38:15 -04:00
zzh
zzh
clintval
Heng Li
Heng Li
Nils Homer
Nils Homer
Andreas Tille
John Marshall
José Manuel Abuín Mosquera