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
04745dd1a8
忽略sam文件
2024-02-22 01:32:18 +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
zzh
293f3bb80e
添加了fmt_idx文件，开始改进seed过程
2023-12-25 11:11:19 +08:00
zzh
d636907248
第一次merge
2023-12-24 17:25:55 +08:00
zzh
44fe799773
添加了一些注释
2023-12-24 17:23:14 +08:00
zzh
7807c96882
Initial commit
2023-12-24 17:21:30 +08:00
e000ecbf45
Merge pull request #367 from martin-g/github-actions-linux-aarch64
...
Add CI job for Ubuntu 20.04 aarch64
2022-09-22 19:52:12 -04:00
370bd3ca25
Add CI job for Ubuntu 20.04 aarch64
...
Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
2022-09-01 10:11:22 +03:00
f89e937d34
Merge pull request #359 from jmarshall/neon
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Add ARM Neon and scalar implementations of SIMD functions
2022-08-31 09:50:31 -04:00
aeff0eed7a
Use native SSE2 intrinsics on i386 as well as x86-64
...
Make the native SSE2 code conditional on __SSE2__, which is defined
by GCC/Clang/etc on x86-64 by default and on i386 with -msse2 etc.
2022-06-27 14:15:59 +01:00
50f99b6890
On other platforms, emulate SSE2 SIMD calls using scalar code
2022-06-26 19:38:20 +01:00
b64ccddda7
On ARM, rewrite SSE2 SIMD calls using Neon intrinsics
...
Many Intel intrinsics have a corresponding Neon equivalent.
Other cases are more interesting:
* Neon's vmaxvq directly selects the maximum entry in a vector,
so can be used to implement both the __max_16/__max_8 macros
and the _mm_movemask_epi8 early loop exit. Introduce additional
helper macros alongside __max_16/__max_8 so that the early loop
exit can similarly be implemented differently on the two platforms.
* Full-width shifts can be done via vextq. This is defined close to
the ksw_u8()/ksw_i16() functions (rather than in neon_sse.h) as it
implicitly uses one of their local variables.
* ksw_i16() uses saturating *signed* 16-bit operations apart from
_mm_subs_epu16; presumably the data is effectively still signed but
we wish to keep it non-negative. The ARM intrinsics are more careful
about type checking, so this requires an extra U16() helper macro.
2022-06-20 20:43:17 +01:00
b5f4bdae91
Make _mm_load_si128() explicit
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The previous code implicitly caused a load; change it so the load
intrinsic is explicitly invoked, as the others are. (This in fact
makes no difference to the generated code.)
2022-06-17 18:42:07 +01:00
0028f086d8
Merge pull request #355 from clintval/cv_document_new_XB
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Document that the XB tag now contains the mapping quality too
2022-06-03 15:01:14 -04:00
c7c2e6ddf7
Document that the XB tag now contains the mapping quality too
2022-05-19 13:43:22 -04:00
8fdc96b5cf
Merge pull request #263 from jmarshall/std-vars
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Makefile: Use $CPPFLAGS and $LDFLAGS if they are set
2022-03-07 09:50:23 -05:00
be36d981cd
Use $CPPFLAGS and $LDFLAGS if they are set
...
The bwa makefile doesn't set these two itself, but the environment
or make command line might set any of CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS.
Use $(CPPFLAGS) when compiling and $(LDFLAGS) when linking so they can
be used to customise the build. Remove $(DFLAGS) from link commands as
these preprocessor options are irrelevant for linking.
2022-03-07 10:59:42 +00:00
59cac0131a
Merge branch 'fulcrumgenomics-feature/add-xa-drop-ratio-option'
2022-03-06 18:22:02 -05:00
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
5d250d35de
Merge pull request #293 from nh13/patch-2
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Output mapping quality with XB
2022-03-06 18:18:45 -05:00
e679702118
Merge pull request #292 from nh13/patch-1
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Document "-u"
2022-03-06 18:16:09 -05:00
4d8fb2ca91
Merge pull request #297 from nh13/patch-3
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Clarify bwa mem -5 option
2022-03-06 18:12:09 -05:00
d26eb2d288
Merge pull request #330 from nh13/patch-4
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Add the mate mapping quality tag
2022-03-06 18:07:01 -05:00
4a18837bd2
Merge pull request #336 from nh13/patch-5
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Add the header line to the output SAM
2022-03-06 18:06:38 -05:00
d47f12cddc
Merge pull request #343 from nh13/patch-7
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Update bwa.1 to remove ancient reference to picard
2022-03-06 18:05:46 -05:00
e43eace9e5
Update bwa.1
2022-02-18 13:36:09 -08:00
56026158d8
Add the header line to the output SAM
...
In particular, this defines the output SAM to be unsorted BUT also query grouped. The latter is very important to explicitly define so downstream tools that don't make assumptions know that reads from the same template are grouped.
2021-12-14 08:02:05 -07:00
f5e83701ab
Add the mate mapping quality tag
2021-07-21 11:12:27 -07:00
d587a9561b
fixed wrong Markdown format in README
2021-05-10 12:48:45 -04:00
b1ab735f7c
updated to Github CI status
2021-05-10 12:47:13 -04:00
7fe5a14058
Merge pull request #325 from jmarshall/ci
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Use GitHub Actions instead of Travis CI
2021-05-10 12:44:43 -04:00
d27d6a520b
Convert Travis CI to GitHub Actions
...
Make an equivalent GitHub Actions workflow that tests compilation
with both GCC and Clang.
2021-05-09 22:54:58 +01:00
zzh
zzh
Heng Li
Martin Tzvetanov Grigorov
John Marshall
clintval
John Marshall
Heng Li
Nils Homer