| 139f68f | Heng Li | 22 September 2022, 23:52:12 UTC | Merge pull request #367 from martin-g/github-actions-linux-aarch64 Add CI job for Ubuntu 20.04 aarch64 | 22 September 2022, 23:52:12 UTC |
| 94248a8 | Martin Tzvetanov Grigorov | 10 August 2022, 11:59:32 UTC | Add CI job for Ubuntu 20.04 aarch64 Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org> | 01 September 2022, 07:11:22 UTC |
| 2e603e4 | Heng Li | 31 August 2022, 13:50:31 UTC | Merge pull request #359 from jmarshall/neon Add ARM Neon and scalar implementations of SIMD functions | 31 August 2022, 13:50:31 UTC |
| c77ace7 | John Marshall | 27 June 2022, 13:15:59 UTC | 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. | 27 June 2022, 13:15:59 UTC |
| ac612b6 | John Marshall | 22 June 2022, 17:47:04 UTC | On other platforms, emulate SSE2 SIMD calls using scalar code | 26 June 2022, 18:38:20 UTC |
| 165e524 | John Marshall | 17 June 2022, 18:34:14 UTC | 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. | 20 June 2022, 19:43:17 UTC |
| ab01ab4 | John Marshall | 17 June 2022, 17:42:07 UTC | Make _mm_load_si128() explicit 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.) | 17 June 2022, 17:42:07 UTC |
| b56db22 | Heng Li | 03 June 2022, 19:01:14 UTC | Merge pull request #355 from clintval/cv_document_new_XB Document that the XB tag now contains the mapping quality too | 03 June 2022, 19:01:14 UTC |
| 2160a0c | clintval | 19 May 2022, 17:43:22 UTC | Document that the XB tag now contains the mapping quality too | 19 May 2022, 17:43:22 UTC |
| 2d4272b | Heng Li | 07 March 2022, 14:50:23 UTC | Merge pull request #263 from jmarshall/std-vars Makefile: Use $CPPFLAGS and $LDFLAGS if they are set | 07 March 2022, 14:50:23 UTC |
| ceaaa6d | John Marshall | 15 December 2019, 18:14:49 UTC | 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. | 07 March 2022, 10:59:42 UTC |
| 8c92aef | Heng Li | 06 March 2022, 23:22:02 UTC | Merge branch 'fulcrumgenomics-feature/add-xa-drop-ratio-option' | 06 March 2022, 23:22:02 UTC |
| 58e3ed2 | Heng Li | 06 March 2022, 23:21:49 UTC | Merge branch 'feature/add-xa-drop-ratio-option' of https://github.com/fulcrumgenomics/bwa into fulcrumgenomics-feature/add-xa-drop-ratio-option | 06 March 2022, 23:21:49 UTC |
| 41e0078 | Heng Li | 06 March 2022, 23:18:45 UTC | Merge pull request #293 from nh13/patch-2 Output mapping quality with XB | 06 March 2022, 23:18:45 UTC |
| cb7e5df | Heng Li | 06 March 2022, 23:16:09 UTC | Merge pull request #292 from nh13/patch-1 Document "-u" | 06 March 2022, 23:16:09 UTC |
| 40b3aee | Heng Li | 06 March 2022, 23:12:09 UTC | Merge pull request #297 from nh13/patch-3 Clarify bwa mem -5 option | 06 March 2022, 23:12:09 UTC |
| 0747fcc | Heng Li | 06 March 2022, 23:07:01 UTC | Merge pull request #330 from nh13/patch-4 Add the mate mapping quality tag | 06 March 2022, 23:07:01 UTC |
| ef52b4a | Heng Li | 06 March 2022, 23:06:38 UTC | Merge pull request #336 from nh13/patch-5 Add the header line to the output SAM | 06 March 2022, 23:06:38 UTC |
| 760098d | Heng Li | 06 March 2022, 23:05:46 UTC | Merge pull request #343 from nh13/patch-7 Update bwa.1 to remove ancient reference to picard | 06 March 2022, 23:05:46 UTC |
| 4bf3cdf | Nils Homer | 18 February 2022, 21:36:09 UTC | Update bwa.1 | 18 February 2022, 21:36:09 UTC |
| 6b18630 | Nils Homer | 14 December 2021, 15:02:05 UTC | 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. | 14 December 2021, 15:02:05 UTC |
| d8dd308 | Nils Homer | 21 July 2021, 18:12:27 UTC | Add the mate mapping quality tag | 21 July 2021, 18:12:27 UTC |
| 3ddd7b8 | Heng Li | 10 May 2021, 16:48:45 UTC | fixed wrong Markdown format in README | 10 May 2021, 16:48:45 UTC |
| fe209ff | Heng Li | 10 May 2021, 16:47:13 UTC | updated to Github CI status | 10 May 2021, 16:47:13 UTC |
| f033d4e | Heng Li | 10 May 2021, 16:44:43 UTC | Merge pull request #325 from jmarshall/ci Use GitHub Actions instead of Travis CI | 10 May 2021, 16:44:43 UTC |
| 765fac1 | John Marshall | 09 May 2021, 21:54:58 UTC | Convert Travis CI to GitHub Actions Make an equivalent GitHub Actions workflow that tests compilation with both GCC and Clang. | 09 May 2021, 21:54:58 UTC |
| fbfffc9 | Heng Li | 22 April 2021, 21:35:37 UTC | added code of conduct | 22 April 2021, 21:35:37 UTC |
| 34374c5 | Heng Li | 09 March 2021, 13:56:52 UTC | Removed the debug output; resolves #320 | 09 March 2021, 13:56:52 UTC |
| 110bf9b | Heng Li | 09 March 2021, 05:52:20 UTC | deprecate bwasw | 09 March 2021, 05:52:20 UTC |
| f1d1fd7 | Heng Li | 23 February 2021, 15:43:41 UTC | output more memory information | 23 February 2021, 15:43:41 UTC |
| b9accf9 | Heng Li | 23 February 2021, 04:26:03 UTC | debug flag to measure memory | 23 February 2021, 04:26:03 UTC |
| 84b2abb | Nils Homer | 19 August 2020, 06:01:43 UTC | 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 | 19 August 2020, 06:01:43 UTC |
| 50122be | Nils Homer | 12 August 2020, 16:01:44 UTC | allow the user to specify the XA drop ratio via the -z option | 12 August 2020, 16:01:44 UTC |
| ab9e0e0 | Nils Homer | 12 August 2020, 15:51:19 UTC | Update fastmap.c | 12 August 2020, 15:51:19 UTC |
| e050ec9 | Nils Homer | 06 August 2020, 17:10:58 UTC | Output mapping quality with XB | 06 August 2020, 17:10:58 UTC |
| e598572 | Nils Homer | 06 August 2020, 17:08:29 UTC | Document "-u" | 06 August 2020, 17:08:29 UTC |
| 13b5637 | Heng Li | 02 July 2020, 17:49:42 UTC | added the MIT license header to main.c | 02 July 2020, 17:49:42 UTC |
| c4a010d | Heng Li | 02 July 2020, 03:02:31 UTC | Merge branch 'master' of github.com:lh3/bwa | 02 July 2020, 03:02:31 UTC |
| 436aceb | Heng Li | 02 July 2020, 03:02:01 UTC | added MIT license to some non-GPL source files | 02 July 2020, 03:02:01 UTC |
| 3072c80 | Heng Li | 23 March 2020, 12:56:40 UTC | Merge pull request #267 from SoapGentoo/fixes GCC 10 and Makefile fixes | 23 March 2020, 12:56:40 UTC |
| 2a1ae7b | David Seifert | 26 February 2020, 12:24:17 UTC | Fix building against GCC 10 * GCC 10 defaults to `-fno-common`, which makes C behave more like C++ in that you can only ever have one definition of an object per executable. | 26 February 2020, 12:24:17 UTC |
| 3a2b0c0 | Heng Li | 09 July 2019, 19:44:34 UTC | updated badges | 09 July 2019, 19:44:34 UTC |
| 38e751a | Heng Li | 09 July 2019, 14:25:57 UTC | mention bwa-mem2 | 09 July 2019, 14:25:57 UTC |
| 20d0a13 | Heng Li | 23 January 2019, 18:23:25 UTC | r1198: exit if .alt is malformatted Resolves #232 | 23 January 2019, 18:28:11 UTC |
| f090f93 | Heng Li | 10 April 2018, 19:01:35 UTC | Merge remote-tracking branch 'origin/master' | 10 April 2018, 19:01:35 UTC |
| e624290 | Heng Li | 07 April 2018, 22:03:10 UTC | Merge pull request #190 from ihaque-freenome/bwa-postalt-fix Bug/patch: bwa-postalt.js writes invalid output for SAM input that is an exact multiple of 65536 bytes in length | 07 April 2018, 22:03:10 UTC |
| 27dd1da | Imran Haque | 07 April 2018, 07:47:32 UTC | Exclude empty SAM lines in bounds check for ALT postprocessor | 07 April 2018, 07:47:32 UTC |
| 11d53b0 | Heng Li | 02 April 2018, 14:47:45 UTC | Merge branch 'dev' into XB | 02 April 2018, 14:47:45 UTC |
| eb7dbc1 | Heng Li | 02 April 2018, 14:43:41 UTC | optionally write XB to include alignment score request from 4DN-DCIC | 02 April 2018, 14:43:41 UTC |
| fde1fd7 | Heng Li | 07 November 2017, 00:51:01 UTC | emphasize pacbio and nanopore | 07 November 2017, 00:51:01 UTC |
| eef0427 | Heng Li | 07 November 2017, 00:49:19 UTC | wording changes | 07 November 2017, 00:49:19 UTC |
| 1a2b0c0 | Heng Li | 07 November 2017, 00:43:02 UTC | fixed a typo in link | 07 November 2017, 00:43:02 UTC |
| 824e00e | Heng Li | 07 November 2017, 00:41:53 UTC | formatting change | 07 November 2017, 00:41:53 UTC |
| ab64326 | Heng Li | 07 November 2017, 00:40:42 UTC | claim bwa-mem long-read mode deprecated | 07 November 2017, 00:40:42 UTC |
| 9f26bfc | Heng Li | 23 October 2017, 17:10:17 UTC | Released bwa-0.7.17 (r1188) | 23 October 2017, 17:10:17 UTC |
| b582816 | Heng Li | 26 September 2017, 13:35:19 UTC | r1187: a typo in command line help | 26 September 2017, 13:35:19 UTC |
| 340babd | Heng Li | 11 September 2017, 13:58:41 UTC | r1185: don't lower supp mapq with -5 | 11 September 2017, 13:58:41 UTC |
| a9c688a | Heng Li | 31 July 2017, 11:55:35 UTC | r1181: fixed a segfault (#145) due to (#138) | 31 July 2017, 11:55:35 UTC |
| 47d9fb2 | Heng Li | 31 July 2017, 02:35:38 UTC | Release 0.7.16-r1180 | 31 July 2017, 02:35:38 UTC |
| 5d15c8b | Heng Li | 30 July 2017, 23:14:09 UTC | Merge pull request #129 from lexentbio/bwakit_fix_sort Fix output file parameter for samtools sort | 30 July 2017, 23:14:09 UTC |
| 950ea8c | Heng Li | 30 July 2017, 23:05:47 UTC | Merge pull request #138 from nh13/nh_mem_mate_cigar Mem should set the mate cigar tag. | 30 July 2017, 23:05:47 UTC |
| 83260cc | Heng Li | 30 July 2017, 22:59:11 UTC | Merge pull request #60 from jdagilliland/typo Typos, doc improvements in man page | 30 July 2017, 22:59:11 UTC |
| 1eee77a | Heng Li | 30 July 2017, 22:56:39 UTC | Merge pull request #84 from jblachly/readgroupfix Forbid literal TAB control characters in @RG line | 30 July 2017, 22:56:39 UTC |
| 24a8d66 | Heng Li | 30 July 2017, 22:49:06 UTC | removed drone.io | 30 July 2017, 22:49:06 UTC |
| 89a5c0c | Heng Li | 30 July 2017, 22:47:03 UTC | moved BWTFree() into BWTIncFree() BWTFree() is not for build. Only BWTIncFree() is needed. | 30 July 2017, 22:47:03 UTC |
| 0976272 | Heng Li | 30 July 2017, 22:36:07 UTC | Merge pull request #139 from jmarshall/fixes Various collected fixes (updated versions of several existing PRs) | 30 July 2017, 22:36:07 UTC |
| a54e769 | Heng Li | 30 July 2017, 21:01:27 UTC | Merge pull request #70 from rmzelle/patch-1 Update README.md | 30 July 2017, 21:01:27 UTC |
| 31bf49d | Heng Li | 30 July 2017, 20:57:30 UTC | Merge pull request #96 from jpfeil/master Add -M option to run-bwamem | 30 July 2017, 20:57:30 UTC |
| 4989736 | Heng Li | 30 July 2017, 20:55:39 UTC | Merge pull request #123 from bwlang/patch-1 updates grch38 URL | 30 July 2017, 20:55:39 UTC |
| 87ed015 | Heng Li | 30 July 2017, 20:53:04 UTC | Merge pull request #141 from jmarshall/bwasw-nan Fail to infer insert size distribution when no pairs are within boundaries (re issue 108) | 30 July 2017, 20:53:04 UTC |
| c56c2e4 | Andreas Tille | 12 July 2015, 12:59:23 UTC | Several trivial Debian patches [Andreas Tille] Check exact number of arguments of bwtupdate Fix spelling [Fabian Klötzl] change printing as size_t is unsigned | 04 July 2017, 20:24:15 UTC |
| 3b96dce | Nils Homer | 25 June 2017, 15:02:42 UTC | Mem should set the mate cigar tag. | 03 July 2017, 15:51:00 UTC |
| bcb475c | John Marshall | 30 June 2017, 12:36:16 UTC | In bsw2_stat(), fail to infer when no pairs are within boundaries Just as we set r.failed and return early if there are no high-quality read pairs at all, also do so if there are none within the calculated boundaries. This avoids returning avg=NAN std=NAN, which leads to malloc(INFINITY) and a crash; fixes #108. | 03 July 2017, 12:42:11 UTC |
| 6906498 | John Marshall | 30 June 2017, 11:46:56 UTC | Copy the whole kstring_t even if it contains NULs FASTQ files containing NULs are invalid but should not cause bwa to crash, as it does if the quality line contains a NUL. Fixes #122. | 30 June 2017, 11:46:56 UTC |
| a61b1dc | John Marshall | 29 June 2017, 14:36:46 UTC | Expand tot_seqs variable to long long This counter is only used in a log message. Fixes #131. | 29 June 2017, 14:36:46 UTC |
| 5ede7eb | Rintze M. Zelle | 10 June 2016, 15:15:53 UTC | Update README.md Correct header formatting, fix some typos in headers | 28 June 2017, 11:07:27 UTC |
| bc58bf2 | John Marshall | 27 June 2017, 16:05:44 UTC | 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. | 27 June 2017, 16:05:44 UTC |
| d28da05 | José Manuel Abuín Mosquera | 24 March 2015, 09:35:46 UTC | Added option to write output to file | 27 June 2017, 15:47:13 UTC |
| ab3a92b | John Marshall | 26 June 2017, 09:45:13 UTC | Prevent Clang warnings on abs() and fabs() calls In the bwa.c and bwase.c calls, rlen is an int64_t returned from bns_get_seq() and is the number of reference bases covered by the alignment; l_query/len is an int and the query length of the alignment; and the result is an int given to an int parameter of ksw_global[2](). As even the result is int and as rlen is effectively bounded by the maximum length of a reference sequence, we maintain the status quo in this code and simply cast rlen to int to silence Clang's "use llabs()" (llabs() would not be a great answer given an int64_t anyway). The bwtsw2_pair.c call needs to remain fabs() so both divisions are done in floating point; cast to double to prevent Clang suggesting changing the call to integer abs(). | 26 June 2017, 09:45:13 UTC |
| 05c5013 | Heng Li | 08 June 2017, 20:06:37 UTC | Merge branch 'dev' | 08 June 2017, 20:06:37 UTC |
| 298284d | Heng Li | 08 June 2017, 20:06:13 UTC | r1144: output debugging message to stderr | 08 June 2017, 20:06:13 UTC |
| 7a77cc4 | Ram Yalamanchili | 18 May 2017, 22:23:05 UTC | Fix output file parameter for samtools sort samtools sort v0.7.15+ requires -o flag to specify the output file | 18 May 2017, 22:42:25 UTC |
| 6a5caf7 | Gwen Ives | 09 December 2014, 09:24:46 UTC | Fixed BWTIncFree() memory leaks [Based on PR #37 with the additions below.] Don't free non-malloced items in BWTFree(). If BWTCreate() is ever called with a non-NULL decodeTable, BWTFree() will need to not free decodeTable -- see FIXME comment. Close packedFile in BWTIncConstructFromPacked() in the normal case. Ignore it in error cases, as they immediately call exit() anyway. | 12 May 2017, 15:34:57 UTC |
| 1972a97 | John Marshall | 10 May 2017, 18:47:12 UTC | Only realloc(pac,...) if it needs to be made larger Similarly to the realloc(pac,...) within add1(), only bother to call realloc() if appending the reverse complemented sequence requires more space than is currently in the pac/m_pac buffer. Avoids realloc(pac,0) (and a "Failed to allocate 0 bytes at bntseq.c" message from wrap_realloc()) in the corner case of an empty reference FASTA file. Fixes #54. | 10 May 2017, 18:47:12 UTC |
| 6442d00 | Brad Langhorst | 27 April 2017, 12:40:48 UTC | updates grch38 URL simple URL update for grch38 fixes #111, #115 grch37 link is still valid | 27 April 2017, 12:40:48 UTC |
| beff2e2 | John Marshall | 25 April 2017, 12:54:31 UTC | Add missing <stdint.h> include Fixes compilation on non-glibc platforms, e.g., FreeBSD and Alpine Linux. | 25 April 2017, 12:54:31 UTC |
| af87825 | John Marshall | 25 April 2017, 12:51:52 UTC | Replace u_int32_t by the more common uint32_t The u_int32_t type comes from <sys/types.h>, which is often included as a byproduct of other headers on glibc platforms, but not on FreeBSD or Alpine Linux. Use <stdint.h>'s uint32_t instead, which is used elsewhere in bwa source code. | 25 April 2017, 12:51:52 UTC |
| 9dfb970 | Jacob Pfeil | 08 November 2016, 00:52:54 UTC | Add -M option to bwakit | 09 November 2016, 19:36:55 UTC |
| 8cc02ba | James Blachly | 09 August 2016, 21:05:51 UTC | Forbid literal TAB control characters in @RG line | 09 August 2016, 21:05:51 UTC |
| 00e59dd | Rintze M. Zelle | 10 June 2016, 15:15:53 UTC | Update README.md Correct header formatting, fix some typos in headers | 10 June 2016, 15:15:53 UTC |
| 5961611 | Heng Li | 31 May 2016, 15:02:54 UTC | Merge branch 'dev' | 31 May 2016, 15:02:54 UTC |
| f123871 | Heng Li | 31 May 2016, 15:01:36 UTC | r1142: added option -5 for Hi-C data | 31 May 2016, 15:01:36 UTC |
| 0876421 | Heng Li | 31 May 2016, 13:43:16 UTC | Merge branch 'dev' | 31 May 2016, 13:43:16 UTC |
| 850dd81 | Heng Li | 31 May 2016, 13:42:50 UTC | Release bwa-0.7.15-r1140 | 31 May 2016, 13:42:50 UTC |
| bdfb9ef | Heng Li | 20 May 2016, 22:06:03 UTC | Merge branch 'dev' | 20 May 2016, 22:06:03 UTC |
| 58bcc25 | Heng Li | 20 May 2016, 22:05:15 UTC | r1138: fixed typo in insert size estimate (#65) credit to @sjackman | 20 May 2016, 22:05:15 UTC |
| ee730f3 | Heng Li | 04 May 2016, 18:41:53 UTC | Merge branch 'dev' | 04 May 2016, 18:41:53 UTC |
| 5db0c36 | Heng Li | 04 May 2016, 18:41:37 UTC | Release 0.7.14-r1136 | 04 May 2016, 18:41:37 UTC |
| fe545f6 | Heng Li | 03 May 2016, 15:29:43 UTC | Merge branch 'dev' | 03 May 2016, 15:29:43 UTC |
| 7ec3261 | Heng Li | 03 May 2016, 15:28:58 UTC | r1134: use AH:* instead of AH:Y | 03 May 2016, 15:28:58 UTC |
