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• b97620afed moved gettimeofday() to misc.c Heng Li 2017-09-02 17:40:10 -04:00
• 743d26eab0 Merge pull request #20 from nanoporetech/msvc14 Heng Li 2017-09-02 14:35:02 -07:00
• 62535ecd7f Merge branch 'dev' Heng Li 2017-09-01 10:06:21 -07:00
• 40665d1083 Merge pull request #23 from simonrharris/segfaultfix Heng Li 2017-09-02 00:46:55 +08:00
• 4db1c0295c Fixed segfault caused when reading from index file Simon Harris 2017-09-01 15:41:21 +01:00
• d4074874ee r316: get rid of a harmless gcc warning Heng Li 2017-09-01 20:25:27 +08:00
• eccdb3a1ca r315: added getopt from musl Heng Li 2017-09-01 20:20:34 +08:00
• a3c3db6b9b ONT source code changes to compile with MSVC 14 Stefan von Deylen 2017-08-30 16:25:20 +01:00
• c4080aaf7e Merge branch 'master' into short Heng Li 2017-08-28 07:02:22 +08:00
• 2641613686 various minor improvements Heng Li 2017-08-25 17:56:16 +08:00
• 5f96d851a8 added spliced alignment example Heng Li 2017-08-25 14:11:54 +08:00
• bf8246f872 Release minimap2-2.1-r311 v2.1 Heng Li 2017-08-25 13:35:55 +08:00
• 5cbd776651 test data for spliced alignment Heng Li 2017-08-25 13:17:56 +08:00
• 0fe1a224ab r309: improved SAM header output Heng Li 2017-08-25 10:35:58 +08:00
• 240f6caaff backup manuscript Heng Li 2017-08-24 22:05:14 +08:00
• b8bdac7e64 backup Heng Li 2017-08-22 17:45:01 +08:00
• 19e4b2aab0 backup Heng Li 2017-08-20 22:10:03 +08:00
• ce859dbe1c evaluate introns Heng Li 2017-08-20 21:54:59 +08:00
• a4c41f64a5 the final version Heng Li 2017-08-20 21:54:35 +08:00
• 5ed2faf270 minor tuning to the matching rules Heng Li 2017-08-19 16:21:49 +08:00
• 8058c85b72 moved appendix to methods; detailed splice aln Heng Li 2017-08-18 23:33:57 +08:00
• 993a2bb521 r301: separate introns from deletions Heng Li 2017-08-18 15:31:15 +08:00
• 64c1389e1a Merge branch 'master' into splice Heng Li 2017-08-17 23:39:27 +08:00
• 81cff97208 r299: support -h: output to stdout; return 0 Heng Li 2017-08-17 23:38:31 +08:00
• bbb37d95f2 support inserting RG lines Heng Li 2017-08-17 23:34:09 +08:00
• 2cde8d257c r297: bidirectional RNA alignment Heng Li 2017-08-17 06:02:44 -04:00
• b5f5929bf9 r296: expose splicing related options to CLI Heng Li 2017-08-13 21:37:51 -04:00
• 28f86688ab r295: gap closure from the middle of non-HPC k Heng Li 2017-08-12 23:48:43 -04:00
• 43506edbc5 backup: preliminary boundary alignment Heng Li 2017-08-12 23:10:14 -04:00
• bcfe00d2ad minor formatting changes Heng Li 2017-08-12 19:09:33 -04:00
• 17c19e5819 exts2 working Heng Li 2017-08-12 19:06:59 -04:00
• 61eef0575c separate out spliced alignment; not right yet Heng Li 2017-08-12 18:54:32 -04:00
• 53b3265d84 r290: in techrep, explain spliced alignment Heng Li 2017-08-12 15:40:49 -04:00
• a23df2dc91 r289: changed CLI help only Heng Li 2017-08-12 12:40:07 -04:00
• 5a74088b74 r288: changed max intron length to 200k Heng Li 2017-08-12 12:39:21 -04:00
• d240318741 r287: refined CLI options and manpage Heng Li 2017-08-12 12:26:04 -04:00
• 0f4c823b0c r286: ignore introns when computing max seg score Heng Li 2017-08-12 10:58:16 -04:00
• 2d11aaa830 option to print all exons for debugging Heng Li 2017-08-12 10:04:16 -04:00
• 30b8cb4672 option to print correct exons Heng Li 2017-08-11 17:50:21 -04:00
• 0c1760bc86 bugfix; print errors; better rules Heng Li 2017-08-11 16:28:52 -04:00
• a99358bc3d r282: reduced intron cost; added eval script Heng Li 2017-08-11 00:06:01 -04:00
• 163fa36ee6 r281: don't open long gaps on query Heng Li 2017-08-10 15:04:59 -04:00
• c59b0781bc r280: output introns as "N" in the cdna mode Heng Li 2017-08-09 11:45:02 -04:00
• 7429b12164 Merge branch 'master' into cdna Heng Li 2017-08-08 22:00:24 -04:00
• 9e1125edda r277: abort if query/-d missing (#11) Heng Li 2017-08-08 21:46:15 -04:00
• 4db0d1034b Show travis CI status Heng Li 2017-08-08 21:32:56 -04:00
• 3dbe23b34e Merge branch 'dev' Heng Li 2017-08-08 21:30:32 -04:00
• 6840370f3c Release minimap2-2.0 (r275) v2.0 Heng Li 2017-08-08 21:16:25 -04:00
• 7f9f659b6a r274: CLI option to change max ref gap Heng Li 2017-08-08 11:39:23 -04:00
• 1a7d782131 r273: cdna mapping mode for testing Heng Li 2017-08-08 11:31:49 -04:00
• 4badf2fcbf avoid wasted memory allocation for backtrack Heng Li 2017-08-08 11:29:46 -04:00
• 079ec0d283 r271: added "short" preset; for testing only Heng Li 2017-08-07 15:30:05 -04:00
• 0137d0dfab command lines used for read simulation Heng Li 2017-08-07 13:41:40 -04:00
• 5b10667967 sim-eval.js to support mason2 read names and SAM Heng Li 2017-08-07 13:28:33 -04:00
• bd1541dce1 renamed simulation-related scripts Heng Li 2017-08-07 13:26:25 -04:00
• 1597f2b030 convert mason2 SAM to fastq Heng Li 2017-08-07 12:45:34 -04:00
• ce927d2aee Merge branch 'master' into dev Heng Li 2017-08-07 12:44:07 -04:00
• 8c2917b391 Added citation. Heng Li 2017-08-06 21:30:47 -04:00
• 9fcf8b6315 added basic travis CI Heng Li 2017-08-04 15:33:40 -04:00
• 3217178d4a fixed k8 download page Heng Li 2017-08-04 14:53:00 -04:00
• b40598fa91 added paf2aln.js example Heng Li 2017-08-04 14:51:33 -04:00
• 269b8661b9 minor clarification Heng Li 2017-08-04 14:49:25 -04:00
• 890d7bbd5b added README for misc scripts Heng Li 2017-08-04 14:46:31 -04:00
• 1aca0d5098 copied sam2paf.js here for completeness Heng Li 2017-08-04 14:44:37 -04:00
• 68d99f0edb Merge branch 'cs-tag' into dev Heng Li 2017-08-04 14:31:46 -04:00
• fd66ab5413 blast-like output working Heng Li 2017-08-04 14:31:21 -04:00
• 71f82759af convert paf to maf Heng Li 2017-08-04 13:05:46 -04:00
• 648cdd8a3b minor wording changes Heng Li 2017-08-04 10:21:10 -04:00
• 7e231cfd3a minor wording improvement Heng Li 2017-08-03 21:28:01 -04:00
• 95d3c30ae3 rephrasing a bit to avoid the apparent TeX bug Heng Li 2017-08-03 20:19:00 -04:00
• f57fd8c790 added one transition phrase Heng Li 2017-08-03 18:01:48 -04:00
• c70b20ee6d removed subsubsection Heng Li 2017-08-03 17:58:36 -04:00
• e8d00a8c8c removed trailing ^M Heng Li 2017-08-03 17:20:43 -04:00
• ed4efd77bc minor modifications Heng Li 2017-08-03 12:47:36 -04:00
• 295874ea30 spell check Heng Li 2017-08-03 12:17:58 -04:00
• 9ec5f51afb the first draft Heng Li 2017-08-03 12:12:55 -04:00
• 28ab4d1f72 backup Heng Li 2017-08-02 22:59:58 -04:00
• 6c9390b54a backup Heng Li 2017-08-02 19:52:31 -04:00
• 9306299e4d added benchmark results Heng Li 2017-08-01 15:12:49 -04:00
• 0c563e1868 Merge branch 'dev' into tex Heng Li 2017-08-01 13:53:16 -04:00
• 8b1e36c609 minor tweaks to the evaluation script Heng Li 2017-08-01 13:52:29 -04:00
• d933a263d7 backup Heng Li 2017-08-01 13:29:02 -04:00
• 7542b4b40a Makefile for TeX Heng Li 2017-08-01 10:42:33 -04:00
• d6181de844 added tech notes Heng Li 2017-08-01 10:38:33 -04:00
• 12cea727b8 r238: bugfix to cs - rev sequence not complemented Heng Li 2017-08-01 10:33:21 -04:00
• cd105b47f2 r237: fixed a bug in outputting cs:Z Heng Li 2017-07-31 14:49:39 -04:00
• 35f232c3fa r236: in cs tag, output differences in lowercase Heng Li 2017-07-31 12:17:48 -04:00
• 4c0713ee14 r235: optionally output tag cs in PAF Heng Li 2017-07-31 12:06:49 -04:00
• 46de0fbdad Merge pull request #8 from rikuu/master Heng Li 2017-07-30 15:10:29 -04:00
• 9e09c1ae72 fix self-comparison in index parameter override check Riku Walve 2017-07-30 21:46:25 +03:00
• d8d4d29b68 Release minimap2-2.0rc1-r232 v2.0rc1 Heng Li 2017-07-30 14:32:40 -04:00
• e51dfd0330 added NEWS Heng Li 2017-07-30 14:20:03 -04:00
• 1f78e1ee53 r230: code formatting changes only Heng Li 2017-07-30 12:31:40 -04:00
• 5934d68772 r229: a new way to prevent out-of-band backtrack Heng Li 2017-07-29 23:52:30 -04:00
• fa99d28d34 r228: reduced unnecessary INV alignment Heng Li 2017-07-29 20:21:53 -04:00
• d08b7a0c51 r227: use local alignment for INV alignment Heng Li 2017-07-29 17:40:53 -04:00
• da3db3c095 r226: only try inv alignment for primary Heng Li 2017-07-29 14:09:35 -04:00
• 783ead6f47 r225: removed a debugging line Heng Li 2017-07-29 13:21:38 -04:00
• 19d6ec885e r224: inversion alignment around Z-drop break Heng Li 2017-07-29 13:09:10 -04:00
• 120bebc290 ake Heng Li 2017-07-29 11:01:49 -04:00