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Author SHA1 Message Date
Heng Li e60d78e0b1 Merge branch 'master' into avx 2019-05-01 10:55:18 -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
Heng Li be171aa2dc implemented in exts; testing is the next 2019-04-28 16:47:12 -04:00
Heng Li cdc730d573 gff2bed to output junction BED 2019-04-28 16:47:12 -04:00
Heng Li 6420acca6d BED I/O 2019-04-28 16:47:12 -04:00
John Marshall 371bc9513a SAM TLEN should be 0 when either read is unmapped 
this_rid/this_pos will be copied from r_prev(=r_next)'s values when this
read is unmapped (i.e., r is NULL). In this case, we can write RNEXT as
'=' but should not calculate TLEN from these placeholder values.
Similarly when the mate is unmapped (i.e., r_next is NULL).

Fixes #365.
 2019-04-05 09:36:46 -04:00
Heng Li e9a45a4e1c Merge branch 'master' into avx 2019-03-04 11:15:56 -05:00
Heng Li 169216bfff manpage was wrongly marked as "dirty" 2019-02-28 15:58:12 -05:00
Heng Li 6b391e3373 Release minimap2-2.16 (r922) v2.16 2019-02-28 15:49:24 -05:00
Heng Li 55e39c2d30 r921: output unmapped reads in full PAF 2019-02-27 15:03:19 -05:00
Kevin Chan 90b7b83ec7 fix typo in command line help 2019-02-27 14:46:57 -05:00
Heng Li d431dc0181 r917: added --max-chain-iter to avoid worst case 
Resolves #324
 2019-02-27 14:41:01 -05:00
Heng Li ccf1680aaf make it explicit that -x is preferred for prebuilt 2019-02-27 12:43:33 -05:00
Heng Li ea84fc0a53 r917: fixed a bug in command-line parsing 
Resolves #344
 2019-02-27 11:22:58 -05:00
Heng Li 19208fb06b r916: support long cs in sam-to-paf conversion 2019-02-17 09:35:23 -05:00
Heng Li e02bebd96d r915: fixed a bug caused by the latest change 2019-02-14 10:04:04 -05:00
Heng Li 32ab6ce15b r914: fixed two harmless division by 0 
Resolves #326
 2019-02-12 19:30:49 -05:00
Heng Li 1739a260fb r913: output tag "rl", length of unseedable regs 2019-02-05 14:19:17 -05:00
Heng Li aaf3233818 added mappy.Aligner.seq_names to return seq names 
Resolves #312
 2019-01-29 12:53:20 -05:00
Heng Li 8b05880f73 r911: option -o to output to file (#319) 2019-01-29 10:42:20 -05:00
Heng Li eba237f39d r910: meaningful error message (#320) 
when minimap2 fails to create temporary files
 2019-01-29 10:29:27 -05:00
Heng Li a8e1e3cbb8 updated citation with page numbers 2019-01-26 17:59:36 -05:00
Heng Li 597212b9f3 r908: added an assertion to detect a potential bug 
as in #311
 2019-01-23 11:18:50 -05:00
Heng Li 30abcf3cf9 r907: copy tag "cs" in sam2paf 
Resolves #310
 2019-01-13 17:52:31 -05:00
Heng Li 48e230f40d r906: de tag is wrongly calculated given "N" 
Resolves #309
 2019-01-11 19:39:09 -05:00
Heng Li c404f49569 Release minimap2-2.15 (r905) v2.15 2019-01-10 12:34:45 -05:00
Heng Li cf2bae6e9b r904: fixed a corner-case segfault. Resolves #307. 2019-01-10 09:57:05 -05:00
Heng Li f5e2176bc5 r903: merged extd2_avx512.c into extd2_sse.c 2019-01-01 13:46:30 -05:00
Heng Li 0b4be2996e avx512 working on MT 2019-01-01 13:05:30 -05:00
Heng Li feca68c71d fixed two bugs when computing full score 2019-01-01 11:46:01 -05:00
Heng Li 6d9ce56721 blend was reversed 2019-01-01 10:27:59 -05:00
Heng Li f2f425890d can be compiled on Linux 2019-01-01 10:04:03 -05:00
Heng Li 58f4210dea compiled, but not working 2019-01-01 01:32:43 -05:00
Heng Li a4782c7d7a r897: avx2 working on test/MT-*.fa 
srli/slli behaves differently between SSE2 and AVX2, which is very annoying.
 2018-12-31 10:26:19 -05:00
Heng Li 2a7d071e8b minor equivalent changes 2018-12-30 23:15:07 -05:00
Heng Li 9462da5159 initial avx2 support; not working properly yet 2018-12-30 11:09:44 -05:00
Heng Li 5b2fdfff9c r895: option in asmgene to count autosomal only 2018-12-14 10:36:47 -05:00
Heng Li ea2b1c5b2a r894: added --max-qlen to filter out long query 2018-12-12 12:27:32 -05:00
Heng Li eef1cee9b7 r893: added paftools.js vcfpair 2018-12-01 18:53:03 -05:00
Heng Li 2c52364527 r892: avoid de:f:0.0000 2018-11-24 21:54:28 -05:00
Heng Li 128476efc9 r891: compute gap-compressed divergence 2018-11-24 21:50:49 -05:00
Heng Li 1b3a6a0fe5 r890: removed "register" (#261) 2018-11-19 13:57:31 -05:00