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913 Commits (9e6fdd376b5e6abb4ca7f4540f79eec7b8271a78)

Author SHA1 Message Date
mbrcic 9e6fdd376b Changed sse2neon with SIMDe. Added building non-SIMD version. 2020-04-20 18:28:06 +02:00
Heng Li 29f67a1666 r982: more accurate sum; output errors 2020-04-14 16:18:53 -04:00
Heng Li adde608a42 Merge remote-tracking branch 'refs/remotes/origin/master' 2020-04-14 15:52:57 -04:00
Heng Li f10dff78dc r981: asmgene to check duplicate genes 2020-04-14 15:52:36 -04:00
Jun Aruga d97bba9f27 travis: added arm64 test. 2020-04-13 08:33:03 -04:00
Heng Li 50775362bb r980: support auNGA 2020-04-10 21:36:59 -04:00
Heng Li 0a5e386359 r979: fixed asmgene wrong report. Resolves #581. 2020-04-06 19:57:15 -04:00
Heng Li cb56fb762a Merge branch 'master' of github.com:lh3/minimap2 2020-03-22 19:17:01 -04:00
Heng Li e2451e497a r975: asmstat without CIGAR/NM 2020-03-22 19:16:43 -04:00
Jared Simpson d2de282d21 remove second definition of kstring 2020-03-02 13:18:37 -05:00
Jared Simpson 48cb80ea94 change kstring_t integer storage size 
This is for compatibility with kstring_t in htslib.
 2020-02-28 09:35:51 -05:00
Heng Li 6a4b9f9082 r974: more informative msg on wrong FASTQ records 
Resolves #510
 2020-01-21 10:56:59 -05:00
Heng Li a7a01fe5bd r973: fixed compiling errors caused 2020-01-21 10:43:31 -05:00
Heng Li 9dceae59a0 r972: renamed --alt-diff to --alt-drop 2020-01-21 10:33:39 -05:00
Heng Li 20a3987082 Merge branch 'master' into alt 2020-01-21 09:17:50 -05:00
Heng Li eb3ed6993d support ALT mapping 2020-01-21 09:17:50 -05:00
Heng Li 7996f04008 r972: fixed negative de:f caused by ambiguous base 2020-01-21 09:14:37 -05:00
Heng Li d2e14705e7 r968: allow large mini_batch; resolves #491 2020-01-18 12:24:44 -05:00
Heng Li 24f50f38e8 r967: no duplicated @SQ lines with --split-prefix 
resolves #527 and #400
 2020-01-18 12:01:28 -05:00
Heng Li 04e015d803 r966: minimap2 returns 1 on file failure (#532) 2020-01-18 10:58:59 -05:00
Heng Li 040f74102c r965: added --chain-gap-scale for #540 2020-01-18 10:29:33 -05:00
Heng Li cdb7857841 r963: --junc-bonus not working; resolves #513 2020-01-06 22:03:50 -05:00
Heng Li 3c0d05d272 r962: abort given wrong RG line; resolves #541 2020-01-06 21:53:21 -05:00
Heng Li 47b646acbf r961: print indexed length 2020-01-06 21:13:33 -05:00
Heng Li a79cb3e991 Merge remote-tracking branch 'origin/master' 2019-12-23 17:33:56 -05:00
Heng Li 367aed4271 added the asan and tsan targets to Makefile 2019-12-23 17:33:10 -05:00
xdudiagnoa 081df6ac7d Fix example.c seq read logic 
for every idx should map all input seqs
 2019-11-11 00:46:07 -05:00
Torsten Seemann a3e7a575fb Add splice:hq to --help 2019-11-11 00:45:13 -05:00
Heng Li d90583b83c r954: fixed two potential undef behaviors (#443) 2019-07-18 09:17:08 -04:00
Heng Li 7fc03b0c32 r953: krealloc is buggy 
Its use in minimap2 didn't trigger the bug, so the older minimap2 is still ok.
 2019-07-18 09:13:30 -04:00
John Marshall 20c104ce8d Report errno on file opening failures and I/O errors 
Add the underlying operating system error (usually "No such file" or
"Out of space" respectively, but highly informative when it is not)
to these error messages.
 2019-07-17 09:04:02 -04:00
Marcus Stoiber 238b6bb3ea Fix memory leak in mappy.aligner.map. 2019-07-08 09:50:54 -04:00
Heng Li e026e18439 added the description of "SA" tag. Closes #438 2019-07-01 09:18:33 -04:00
Heng Li 58c2251b18 compatibility with GenBank GTP (resolves $422) 2019-06-11 09:16:03 -04:00
Heng Li 03dc8d5d97 test if index is built for #413 2019-06-07 09:11:11 -04:00
Heng Li 5cb61f8ee6 added FAQ 2019-06-06 10:47:33 -04:00
Heng Li c16a1742a3 Er... Tavis doesn't have python 3.7. 2019-05-11 20:06:48 -04:00
Heng Li 4bd5a018c2 test python 3.7 instead of 3.6 2019-05-11 20:05:06 -04:00
Heng Li 05974c80f1 r943: allow long ref name for --split-index 
Resolved #394.
 2019-05-10 15:39:41 -04:00
Heng Li 7bc87b4175 Release minimap2-2.17 (r941) 2019-05-04 23:49:17 -04:00
Heng Li 6762368cf0 r940: added the splice:hq preset 
for high-quality CCS/mRNA splice alignment
 2019-05-04 14:00:31 -04:00
Heng Li c2aec88b84 r938: added --sam-hit-only; resolved #377 2019-04-30 22:40:36 -04:00
Heng Li 97f67a2a0a r937: enlarge mm_mapopt_t::flag to 64 bits 2019-04-30 22:30:32 -04:00
Heng Li 189555503a potentially fix issue #372 
Needs someone to confirm
 2019-04-30 21:49:51 -04:00
Heng Li 69af86657e r935: fixed a cigar like 5I6D7I; resolved #392 2019-04-30 21:35:24 -04:00
Heng Li 49c6d83a8e r934: --junc-bed to read BED12 2019-04-28 20:12:28 -04:00
Heng Li f64e426a5a r933: resume versioning 2019-04-28 17:05:37 -04:00
Heng Li 2bb8cbbeef updated manpage 2019-04-28 17:02:49 -04:00
Heng Li e80759c97a --junc-bed apparently working 
Also fixed an issue with splice alignment in the reverse strand, though this
should have a very minor effect in practice.
 2019-04-28 16:47:12 -04:00
Heng Li f4c844b143 fixed a few simple bugs and leaks 2019-04-28 16:47:12 -04:00