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  • fb5279120b hybrid index实现seeding过程的初始代码 hyb-main zzh 2025-06-16 10:11:29 +0800
  • 40544d02fe 在gz_read部分加了异步读取 main zzh 2025-01-13 20:24:20 +0800
  • b50360bb48 整合了ert seeding，结果正确，完善了shm zzh 2024-08-06 03:08:10 +0800
  • 364ee9756e 添加了共享内存支持，成功构建ert索引 zzh 2024-08-03 17:26:32 +0800
  • 9c9502d584 clean代码，结果正确 zzh 2024-07-26 04:15:55 +0800
  • 8c2a90e3e2 修改了双线程解压读写fastq.gz的bug，修改了一些测试代码 zzh 2024-06-24 18:11:54 +0800
  • d1a5715e56 将fputs改成fwrite，写入效率提升30% zzh 2024-04-06 20:53:42 +0800
  • d41c038616 清理一些fprintf zzh 2024-04-06 16:08:43 +0800
  • 3e20d7ee0f 解决了创建bwt索引时，一同创建fmt相关的索引相关的bug，现在可以正常一起创建索引了，接下来还可以将sa和bytesa一起创建来减小时间 zzh 2024-04-06 15:05:20 +0800
  • dd7db7beb6 修改一下索引文件后缀名称 zzh 2024-04-02 07:50:22 +0800
  • 123aceb6a6 将fmt和kmer合并到建索引的过程中 zzh 2024-04-02 07:49:38 +0800
  • 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 zzh 2024-04-02 07:42:37 +0800
  • dd03596997 加入了获取reads和extension数据的代码 zzh 2024-03-27 23:47:39 +0800
  • 1e3965cb7d 添加了可同时读写的pipeline，优化了时间统计 zzh 2024-03-24 04:40:09 +0800
  • d728ddbe2c 解决了bsw上边界同样的问题，解决了seed3的一个bug zzh 2024-03-23 03:23:05 +0800
  • 2eaeb26858 添加了直接扩展两个碱基的函数 zzh 2024-03-14 15:32:34 +0800
  • 856a0e0c01 改成了batch模式，对na12878有效果 zzh 2024-03-09 11:39:40 +0800
  • 7d085962a2 开始改成sbwa那种batch模式 zzh 2024-03-07 18:23:21 +0800
  • 6e1dd08fb6 将seed和extend部分修改成了batch模式，好像没啥效果 zzh 2024-02-23 01:09:08 +0800
  • 04745dd1a8 忽略sam文件 zzh 2024-02-22 01:32:18 +0800
  • 4bd0fd4f91 做了一些代码清理，目前结果应该是完全一致的 zzh 2024-02-22 01:26:57 +0800
  • 17618ee5f2 解决了sa的bug，现在结果和原版一模一样 zzh 2024-02-21 15:21:56 +0800
  • 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 zzh 2024-02-20 01:12:02 +0800
  • 4a1c2cd3db 修改一些注释疏忽的问题 zzh 2024-02-16 21:23:55 +0800
  • 7dceae8c5d seed三个步骤，全部用fmt实现，而且结果一致 zzh 2024-02-16 20:59:59 +0800
  • 9d45fd02fb 添加了bit过滤，解决了一些bug，现在seed1和seed2都没问题了 zzh 2024-02-16 00:18:14 +0800
  • 5d8ace386f seed1和seed2结果都正确 zzh 2024-02-13 13:37:07 +0800
  • d41b8da061 kmer长度变为14，结果正确 zzh 2024-02-12 20:54:57 +0800
  • 463f7da138 将smem1函数用fmt结构实现了，结果基本正确 zzh 2024-02-07 22:08:51 +0800
  • bf678f4dae 实现了用33bit表示sa，间隔为4，释放内存的时候会崩溃 zzh 2023-12-27 10:42:12 +0800
  • c981585fd2 添加了运行时间计算代码，用来分析性能 zzh 2023-12-25 13:58:15 +0800
  • 293f3bb80e 添加了fmt_idx文件，开始改进seed过程 zzh 2023-12-25 11:11:19 +0800
  • d636907248 第一次merge zzh 2023-12-24 17:25:55 +0800
  • 44fe799773 添加了一些注释 zzh 2023-12-24 17:23:14 +0800
  • 7807c96882 Initial commit zzh 2023-12-24 17:21:30 +0800
  • e000ecbf45 Merge pull request #367 from martin-g/github-actions-linux-aarch64 Heng Li 2022-09-22 19:52:12 -0400
  • 370bd3ca25 Add CI job for Ubuntu 20.04 aarch64 Martin Tzvetanov Grigorov 2022-08-10 14:59:32 +0300
  • f89e937d34 Merge pull request #359 from jmarshall/neon Heng Li 2022-08-31 09:50:31 -0400
  • aeff0eed7a Use native SSE2 intrinsics on i386 as well as x86-64 John Marshall 2022-06-27 14:15:59 +0100
  • 50f99b6890 On other platforms, emulate SSE2 SIMD calls using scalar code John Marshall 2022-06-22 18:47:04 +0100
  • b64ccddda7 On ARM, rewrite SSE2 SIMD calls using Neon intrinsics John Marshall 2022-06-17 19:34:14 +0100
  • b5f4bdae91 Make _mm_load_si128() explicit John Marshall 2022-06-17 18:42:07 +0100
  • 0028f086d8 Merge pull request #355 from clintval/cv_document_new_XB Heng Li 2022-06-03 15:01:14 -0400
  • c7c2e6ddf7 Document that the XB tag now contains the mapping quality too clintval 2022-05-19 13:43:22 -0400
  • 8fdc96b5cf Merge pull request #263 from jmarshall/std-vars Heng Li 2022-03-07 09:50:23 -0500
  • be36d981cd Use $CPPFLAGS and $LDFLAGS if they are set John Marshall 2019-12-15 18:14:49 +0000
  • 59cac0131a Merge branch 'fulcrumgenomics-feature/add-xa-drop-ratio-option' Heng Li 2022-03-06 18:22:02 -0500
  • 49c397d16e Merge branch 'feature/add-xa-drop-ratio-option' of https://github.com/fulcrumgenomics/bwa into fulcrumgenomics-feature/add-xa-drop-ratio-option Heng Li 2022-03-06 18:21:49 -0500
  • 5d250d35de Merge pull request #293 from nh13/patch-2 Heng Li 2022-03-06 18:18:45 -0500
  • e679702118 Merge pull request #292 from nh13/patch-1 Heng Li 2022-03-06 18:16:09 -0500
  • 4d8fb2ca91 Merge pull request #297 from nh13/patch-3 Heng Li 2022-03-06 18:12:09 -0500
  • d26eb2d288 Merge pull request #330 from nh13/patch-4 Heng Li 2022-03-06 18:07:01 -0500
  • 4a18837bd2 Merge pull request #336 from nh13/patch-5 Heng Li 2022-03-06 18:06:38 -0500
  • d47f12cddc Merge pull request #343 from nh13/patch-7 Heng Li 2022-03-06 18:05:46 -0500
  • e43eace9e5 Update bwa.1 Nils Homer 2022-02-18 13:36:09 -0800
  • 56026158d8 Add the header line to the output SAM Nils Homer 2021-12-14 08:02:05 -0700
  • f5e83701ab Add the mate mapping quality tag Nils Homer 2021-07-21 11:12:27 -0700
  • d587a9561b fixed wrong Markdown format in README Heng Li 2021-05-10 12:48:45 -0400
  • b1ab735f7c updated to Github CI status Heng Li 2021-05-10 12:47:13 -0400
  • 7fe5a14058 Merge pull request #325 from jmarshall/ci Heng Li 2021-05-10 12:44:43 -0400
  • d27d6a520b Convert Travis CI to GitHub Actions John Marshall 2021-05-09 22:54:58 +0100
  • 87e42dbe32 added code of conduct Heng Li 2021-04-22 17:35:37 -0400
  • ddbd5f7fb7 Removed the debug output; resolves #320 Heng Li 2021-03-09 08:56:52 -0500
  • 5b96937edc deprecate bwasw Heng Li 2021-03-09 00:52:20 -0500
  • e2dbfe60e3 output more memory information Heng Li 2021-02-23 10:43:41 -0500
  • d422bdbed9 debug flag to measure memory Heng Li 2021-02-22 23:26:03 -0500
  • b58da139c3 Clarify bwa mem -5 option Nils Homer 2020-08-18 23:01:43 -0700
  • 34caf50d46 allow the user to specify the XA drop ratio via the -z option Nils Homer 2020-08-12 09:01:44 -0700
  • 9cbbd6bf94 Update fastmap.c Nils Homer 2020-08-12 08:51:19 -0700
  • f717ea1318 Output mapping quality with XB Nils Homer 2020-08-06 10:10:58 -0700
  • 1a11a6f4b9 Document "-u" Nils Homer 2020-08-06 10:08:29 -0700
  • 94ff6b297a added the MIT license header to main.c Heng Li 2020-07-02 13:49:42 -0400
  • d13c2af9bd Merge branch 'master' of github.com:lh3/bwa Heng Li 2020-07-01 23:02:31 -0400
  • 02a9add042 added MIT license to some non-GPL source files Heng Li 2020-07-01 23:02:01 -0400
  • 3112df7100 Merge pull request #267 from SoapGentoo/fixes Heng Li 2020-03-23 08:56:40 -0400
  • 2f82fe897a Fix building against GCC 10 David Seifert 2020-02-26 13:24:17 +0100
  • e8e2803a3d updated badges Heng Li 2019-07-09 15:44:34 -0400
  • 9b12309015 mention bwa-mem2 Heng Li 2019-07-09 10:25:57 -0400
  • cd29a7cb54 r1198: exit if .alt is malformatted Heng Li 2019-01-23 13:23:25 -0500
  • e4d7a94252 Merge remote-tracking branch 'origin/master' Heng Li 2018-04-10 15:01:35 -0400
  • f9294c0593 Merge pull request #190 from ihaque-freenome/bwa-postalt-fix Heng Li 2018-04-07 18:03:10 -0400
  • 27dd1da702 Exclude empty SAM lines in bounds check for ALT postprocessor Imran Haque 2018-04-07 07:47:32 +0000
  • 11d53b06fb Merge branch 'dev' into XB Heng Li 2018-04-02 10:47:45 -0400
  • eb7dbc1429 optionally write XB to include alignment score Heng Li 2018-04-02 10:43:41 -0400
  • fde1fd7ce3 emphasize pacbio and nanopore Heng Li 2017-11-06 19:51:01 -0500
  • eef04271e6 wording changes Heng Li 2017-11-06 19:49:19 -0500
  • 1a2b0c001a fixed a typo in link Heng Li 2017-11-06 19:43:02 -0500
  • 824e00e7ac formatting change Heng Li 2017-11-06 19:41:53 -0500
  • ab64326ae6 claim bwa-mem long-read mode deprecated Heng Li 2017-11-06 19:40:42 -0500
  • 9f26bfcc77 Released bwa-0.7.17 (r1188) Heng Li 2017-10-23 13:10:17 -0400
  • b582816211 r1187: a typo in command line help Heng Li 2017-09-26 09:35:19 -0400
  • 340babdd67 r1185: don't lower supp mapq with -5 Heng Li 2017-09-11 09:58:41 -0400
  • a9c688ac92 r1181: fixed a segfault (#145) due to (#138) Heng Li 2017-07-31 07:55:35 -0400
  • 47d9fb27d7 Release 0.7.16-r1180 Heng Li 2017-07-30 22:35:38 -0400
  • 5d15c8b09f Merge pull request #129 from lexentbio/bwakit_fix_sort Heng Li 2017-07-30 19:14:09 -0400
  • 950ea8cf40 Merge pull request #138 from nh13/nh_mem_mate_cigar Heng Li 2017-07-30 19:05:47 -0400
  • 83260ccb10 Merge pull request #60 from jdagilliland/typo Heng Li 2017-07-30 18:59:11 -0400
  • 1eee77ad93 Merge pull request #84 from jblachly/readgroupfix Heng Li 2017-07-30 18:56:39 -0400
  • 24a8d66481 removed drone.io Heng Li 2017-07-30 18:49:06 -0400
  • 89a5c0c5c8 moved BWTFree() into BWTIncFree() Heng Li 2017-07-30 18:47:03 -0400