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  • 3a375d3436 renamed paf2ovlp to ov-eval Heng Li 2017-12-24 18:04:00 -0500
  • 626f10e0d0 evaluate sensitivity in the same script Heng Li 2017-12-24 17:55:42 -0500
  • b997578078 find reads overlaps based on reference alignment Heng Li 2017-12-24 17:20:27 -0500
  • ce8a48d715 fixed two minor typos in references Heng Li 2017-12-24 13:14:47 -0500
  • 99879e9e75 a new section on estimating sequence divergence Heng Li 2017-12-24 12:57:38 -0500
  • c969d1a1ce updated direct RNA-seq results; cite syndip Heng Li 2017-12-24 11:06:17 -0500
  • fcac296c4a clarify ARM-NEON support in README Heng Li 2017-12-18 23:01:44 -0500
  • e420b17496 r629: API to construct index from strings Heng Li 2017-12-18 22:29:46 -0500
  • 23a846c594
         Merge pull request #81 from hasindu2008/master Heng Li 2017-12-16 09:40:41 -0500
  • 8995e2e078 added support for arm neon Hasindu Gamaarachchi 2017-12-15 17:42:19 +1100
  • ab345e600b r626: function to check incorrect scoring system Heng Li 2017-12-13 12:23:43 -0500
  • d003a00d71 r625: HPC sketch still has one minor issue Heng Li 2017-12-13 09:40:42 -0500
  • ae85dcde76 added esterr.o dependencies Heng Li 2017-12-13 09:01:48 -0500
  • eb819c29e8 Release minimap2-2.6 (r623) Heng Li 2017-12-12 10:39:20 -0500
  • fb630de40a r622: fixed bug in sdust due to recent refactor Heng Li 2017-12-11 15:32:28 -0500
  • 43960a8ca7 r621: --print-qname also shows kalloc status Heng Li 2017-12-11 12:30:08 -0500
  • f6608fe99c r620: revamped thread-local memory management Heng Li 2017-12-11 12:11:10 -0500
  • 98a6e52c06 r618: heuristics to avoid tiny terminal exons Heng Li 2017-12-10 21:52:07 -0500
  • 824712a4ee r617: removed some unused code Heng Li 2017-12-10 17:54:50 -0500
  • 0e42628ef6 r611: document --idx-no-seq; better inv aln Heng Li 2017-12-08 13:16:18 -0500
  • 98a999fe44 r611: added pseudocount when est divergence Heng Li 2017-12-08 12:57:57 -0500
  • fec7bd713f r610: warning if db sequence is 0-lengthed (#69) Heng Li 2017-12-07 21:05:39 -0500
  • 2f693e8ca4 r609: bugfix - SDUST masking not working Heng Li 2017-12-07 11:45:38 -0500
  • 704ff9f4c6 r607: estimate sequence divergence Heng Li 2017-12-06 16:14:39 -0500
  • 68c63f2d68 r606: fixed a sketch bug for long 256bp k-mer Heng Li 2017-12-06 16:13:29 -0500
  • 76206f574f support both SAM and PAF as input Heng Li 2017-12-02 21:57:19 -0500
  • e575f884e1 convert spliced PAF to BED Heng Li 2017-12-02 21:23:41 -0500
  • 571161d5a2 changed badges Heng Li 2017-12-01 14:40:18 -0500
  • 07d41efc2b explain secondary/supplementary aln for RNA-seq Heng Li 2017-11-30 23:02:20 -0500
  • 984f7846c0 r601: bugfix - a similar issue to r600 Heng Li 2017-11-30 11:51:34 -0500
  • af1d6afba9 r600: bugfix - missing secondary alignments (#71) Heng Li 2017-11-30 11:34:10 -0500
  • cbdb6c069f when there are incorrect anno, warn but not abort Heng Li 2017-11-24 12:48:49 -0500
  • 35b6d9f7d5 direct manpage to HTML Heng Li 2017-11-24 11:05:20 -0500
  • 39a9666246 convert PAF to LAST's cigar output Heng Li 2017-11-17 09:42:16 -0500
  • 662d05dc02 fixed incorrect var coordinate Heng Li 2017-11-12 20:25:33 -0500
  • 379457c18b use mapq threshold Heng Li 2017-11-12 19:01:34 -0500
  • 03169d590b print cov-1 regions (not BED output any more) Heng Li 2017-11-12 18:45:49 -0500
  • 8c8d446820 find regions covered by one contig Heng Li 2017-11-12 18:41:01 -0500
  • 0ddb064f17 dnadiff-like script; improvement coming Heng Li 2017-11-12 15:07:29 -0500
  • 131cfc6938 r574: build index without sequences Heng Li 2017-11-11 21:38:38 -0500
  • 2f463b1db0 r573: prepare to generalize index Heng Li 2017-11-11 19:54:06 -0500
  • 3b518271ee Release minimap2-2.5 (r572) Heng Li 2017-11-11 11:29:28 -0500
  • 481d8239e9
         Merge pull request #57 from cjw85/strand_typo Heng Li 2017-11-10 20:36:19 -0500
  • 4f77b0c1ed Fix typo in strand property cwright 2017-11-11 01:18:44 +0000
  • d7a31e40e6 r569: last commit is buggy Heng Li 2017-11-09 23:20:41 -0500
  • dd18cd75de r568: revert - don't take max(dp_max, dp_score) Heng Li 2017-11-09 23:12:48 -0500
  • 99a2709913 r567: minor change to #56 Heng Li 2017-11-09 19:17:45 -0500
  • 032068a747
         Merge pull request #56 from mvdbeek/softclipping Heng Li 2017-11-09 19:12:47 -0500
  • 1cb0bf4bef Implement -Y for soft clipping of supp. alignments mvdbeek 2017-11-09 17:14:10 +0100
  • 422b43374e
         Merge pull request #55 from martinghunt/fix_python3_strings Heng Li 2017-11-09 09:37:41 -0500
  • 29a26e3eea Bug fix with byte strings in Python3 martinghunt 2017-11-09 13:57:15 +0000
  • a7b38f6900 r562: fixed a severe bug: wrong query start Heng Li 2017-11-08 22:31:05 -0500
  • e896c9ec05 r559: prefer a chain involving more segments Heng Li 2017-11-08 13:22:16 -0500
  • 98ba8928c6 r558: dp_max no less than dp_score Heng Li 2017-11-08 10:06:10 -0500
  • bcf8462d20
         Merge pull request #52 from cvdelannoy/patch-1 Heng Li 2017-11-08 07:50:31 -0500
  • c047c852ce
         Update README.md Carlos de Lannoy 2017-11-08 13:07:01 +0100
  • b24d68ae9f r557: fixed another mapq underestimate Heng Li 2017-11-07 23:20:49 -0500
  • 65deedfa96 r556: bugfix - underestimate mapq for split aln Heng Li 2017-11-07 22:37:12 -0500
  • 21a46ba652 Release minimap2-2.4 (r555) Heng Li 2017-11-06 12:54:02 -0500
  • 1617b87ee1 this will become version 3 at arXiv Heng Li 2017-11-06 10:57:12 -0500
  • 2191ac58ad two discussion paragraphs; need one more Heng Li 2017-11-05 12:27:52 -0500
  • fa5a645ca5 r552: fixed a tiny typo on struct packing Heng Li 2017-11-05 08:27:26 -0500
  • c2b09356b8 moved conclusion to result; need new discussion Heng Li 2017-11-04 22:19:46 -0400
  • a3f0aa1d5b r550: fixed -L issues with secondary and supp aln Heng Li 2017-11-04 12:13:38 -0400
  • 52ffbc9e0c added bowtie2 and snap versions Heng Li 2017-11-02 15:51:23 -0400
  • a9790c0f1d added two bowtie2 numbers for comparison Heng Li 2017-11-02 15:44:48 -0400
  • d0ac78ac08 updated the tech note Heng Li 2017-11-02 15:37:24 -0400
  • 22290db3e4 r546: minor mapQ tuning Heng Li 2017-11-01 13:20:39 -0400
  • cd24dc8834 r545: removed option -i, not working well Heng Li 2017-10-31 22:23:27 -0400
  • b8e758df0f r544: increased PE mapQ Heng Li 2017-10-31 16:55:02 -0400
  • 311fa90030 r543: applied some sr mapq changes to long reads Heng Li 2017-10-31 15:24:05 -0400
  • fb8a1b5536 r542: tuning mapQ calculation Heng Li 2017-10-31 14:25:09 -0400
  • 7f11f4c4d4 Instructions on different long RNA-seq techs Heng Li 2017-10-29 13:58:25 -0400
  • 285eb0da05 r540: removed a buggy debugging line Heng Li 2017-10-29 00:02:41 -0400
  • 192217a10c r539: use --splice-flank=yes by default Heng Li 2017-10-28 22:29:55 -0400
  • f22a94e868 r538: fixed a long existing bug in HPC k-mer (#47) Heng Li 2017-10-28 19:21:10 -0400
  • 79b0caca95 r537: model the next base to GT/AG Heng Li 2017-10-28 00:25:01 -0400
  • afc2f2e84b r536: removed an unnecessary assert() Heng Li 2017-10-24 21:08:54 -0400
  • e6f66f2f3b disabled download counts Heng Li 2017-10-24 14:40:08 -0400
  • 70735098e2 fixed a typo in README Heng Li 2017-10-24 14:39:33 -0400
  • d4b5dfc297 r533: added --no-pairing Heng Li 2017-10-23 14:09:32 -0400
  • 5acd709524 updated the download link to v2.3 Heng Li 2017-10-23 13:43:31 -0400
  • 306e4541f8 Released minimap2-2.3 (r531) Heng Li 2017-10-22 23:13:35 -0400
  • 1dd221ad82 a bit more on short read mapping Heng Li 2017-10-22 18:38:35 -0400
  • c6b6392b70 minor wording changes Heng Li 2017-10-21 23:46:36 -0400
  • dc37aee881 minor wording changes Heng Li 2017-10-21 23:38:05 -0400
  • 37e627aa98 note on long cigar in README Heng Li 2017-10-21 22:28:06 -0400
  • beeb806829 r526: fixed a bug when HPC is in use Heng Li 2017-10-21 19:54:04 -0400
  • be7f3c4ffe r525: fixed a bug in chaining; handle ovlp ends Heng Li 2017-10-20 21:34:52 -0400
  • bd04372873 r524: reverted to bwa-mem end bonus Heng Li 2017-10-20 16:57:31 -0400
  • 15ed0712c2 r523: fixed a performance bug in ksw2_ll Heng Li 2017-10-20 13:00:10 -0400
  • 55dcbefe87 updated text (unfinished) Heng Li 2017-10-20 12:44:54 -0400
  • 8abba332ad replaced mapQ plot with sr roc Heng Li 2017-10-19 23:43:17 -0400
  • 4683da2455 r520: added option -L to write long cigar to CG Heng Li 2017-10-17 17:32:44 -0400
  • ffd953029f r519: fixed a severe bug that misses long alns Heng Li 2017-10-17 15:52:36 -0400
  • 04cf4ebf5e r518: increased the default -K to 500M Heng Li 2017-10-17 13:21:29 -0400
  • 25ffd72690 r517: replaced --print-2nd with --secondary Heng Li 2017-10-17 11:41:56 -0400
  • aa2d9d4e1b r516: throw a warning if -N0 is used Heng Li 2017-10-16 14:55:35 -0400
  • addb61bcb2 r515: more conservative hit exclusion Heng Li 2017-10-16 13:58:01 -0400
  • b24c9c90c7 updated mappy and example.c Heng Li 2017-10-16 11:15:07 -0400