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  • 70b0fede64 r835: improved help message. Resolved #232 Heng Li 2018-09-14 22:29:25 -04:00
  • 0b681e51e7 Merge remote-tracking branch 'remotes/origin/master' Heng Li 2018-09-14 22:22:20 -04:00
  • 7d80d6de4a r832: fixed outdated -L. Resolved #231 and #233 Heng Li 2018-09-14 22:21:33 -04:00
  • 791e89ce0f PEP8 and other minor styles changes Chris Rands 2018-09-12 16:04:43 +02:00
  • 98c48a1c45 Fixed wrong version links in the cookbook Heng Li 2018-09-03 09:07:34 -04:00
  • 63d397120a removed getopt.c from MANIFEST Heng Li 2018-09-01 21:30:46 -04:00
  • 7998fe9906 r829: replaced musl's getopt with ketopt Heng Li 2018-09-01 21:15:43 -04:00
  • 3a119d606f r828: --MD to support spliced alignment Heng Li 2018-08-22 10:47:45 -04:00
  • a5eafb75f9 Release minimap2-2.12 (r827) v2.12 Heng Li 2018-08-06 12:44:39 -04:00
  • 9a567e4b37 allow mappy to change scoring Heng Li 2018-08-06 09:52:13 -04:00
  • 8e606bcc06 added a -C5 example to Getting Started Heng Li 2018-08-06 09:08:33 -04:00
  • a1b7219b5d explain added parameters Heng Li 2018-08-05 21:32:05 -04:00
  • b0f39a1a61 r823: mappy to index a single sequence Heng Li 2018-08-05 20:57:05 -04:00
  • 5ab6538757 r822: added option --no-end-flt Heng Li 2018-08-05 19:42:12 -04:00
  • b32296e18f r821: fixed memory when -y is used Heng Li 2018-07-31 15:14:37 -04:00
  • 99ecdf7b5d mappy to support arm64 (#203) Heng Li 2018-07-24 23:53:02 -04:00
  • ff9917a1c4 r819: mappy to support cs/MD Heng Li 2018-07-24 23:29:55 -04:00
  • 8c064a5f29 Fixed mm_idx_is_idx to return the correct result on Windows. Mark Bicknell 2018-07-17 10:17:44 +01:00
  • 0e137670fc Merge branch 'split' Heng Li 2018-07-15 22:24:15 -04:00
  • 395c8d678a r815: fixed a memory leak split Heng Li 2018-07-15 22:11:32 -04:00
  • 830da7fa27 r814: resumed versioning Heng Li 2018-07-15 11:48:14 -04:00
  • a655cbef86 print SAM header; remove tmp files Heng Li 2018-07-15 11:03:18 -04:00
  • 4b707aac92 working with toy examples Heng Li 2018-07-15 10:55:00 -04:00
  • 951c0d1d35 apparently mm_append_cigar() wastes some memory Heng Li 2018-07-14 23:47:44 -04:00
  • 3545e35a42 pairing in the split-idx mode Heng Li 2018-07-14 23:43:34 -04:00
  • f3417da838 bugfix: unmapped records are duplicated in output Heng Li 2018-07-14 22:54:05 -04:00
  • e5277dbf5c code backup Heng Li 2018-07-14 22:52:36 -04:00
  • 1a55227d5a write hits to tmp files (unfinished) Heng Li 2018-07-14 12:15:10 -04:00
  • 5cfa621b2d use unmapped records Heng Li 2018-07-07 12:49:15 -05:00
  • a609a07f8c optionally output unmapped query in PAF Heng Li 2018-07-07 10:26:08 -05:00
  • bcf92b3c46 compute query coverage Heng Li 2018-07-06 21:52:01 -05:00
  • 097378ab90 reworked break point counting Heng Li 2018-07-06 09:46:26 -04:00
  • 10bbbe28c5 added asmstat Heng Li 2018-07-05 13:22:32 -04:00
  • c92a6866f3 Release the GIL to allow native Python threading. Hyeshik Chang 2018-06-27 02:09:58 +09:00
  • 6908dc59a5 --splice implied when searching for splicing sites on single strand Maël Kerbiriou 2018-07-04 15:53:27 +02:00
  • 50dae10421 paftools call to show statistics on longer indels Heng Li 2018-07-03 14:28:09 -04:00
  • 0517972d02 Release minimap2-2.11 (r797) v2.11 Heng Li 2018-06-21 00:04:08 -04:00
  • d46e68e6ad r796: don't use ssize_t Heng Li 2018-06-20 12:45:27 -04:00
  • 2584a4149a r295: use -r2000 for ava-ont, NOT for ava-pb Heng Li 2018-06-20 12:24:43 -04:00
  • 66674afd09 r794: fixed a bug in seed filtering Heng Li 2018-06-20 10:26:29 -04:00
  • e9ca0c9dab added __version__; resolved #165 Heng Li 2018-06-19 15:40:26 -04:00
  • 7e6e8ca73f r792: fixed -Wextra warnings and resolved #184 Heng Li 2018-06-19 15:26:58 -04:00
  • 408e098859 fix deserialization of zero-length reference names Ilya Kolpakov 2018-06-06 23:04:59 +02:00
  • 57f37551f8 expose mm_idx_is_idx, mm_idx_load and mm_idx_dump Ilya Kolpakov 2018-06-06 16:26:23 +02:00
  • 4c66b689c3 fix serialization of empty names in mm_idx_dump Ilya Kolpakov 2018-06-06 16:24:25 +02:00
  • 1bde2cf076 Allow setting max_frag_len on a per alignment level mvdbeek 2018-06-04 15:48:54 +02:00
  • 31fc0f218a Allow setting max_frag_len parameter in Aligner class mvdbeek 2018-06-04 15:42:14 +02:00
  • 3d3bcc29a8 Fix CIGAR reallocation with --eqx Aaron Wenger 2018-06-04 12:04:40 -07:00
  • 99dcd75f64 added support for 64 bit ARM architectures Hasindu Gamaarachchi 2018-06-11 14:23:03 +10:00
  • 154d2caf5b r784: support the =/X CIGAR operators (#156) Heng Li 2018-05-30 16:11:22 -04:00
  • a3afeec0b2 r783: reverted to r781 (#155) Heng Li 2018-05-30 15:25:34 -04:00
  • 3573784b4d r782: no mask a chain having long ref ovlp (#155) Heng Li 2018-05-30 13:53:45 -04:00
  • 872f300955 r781: fixed the buggy heapmerge (resolves #166) Heng Li 2018-05-30 11:55:14 -04:00
  • 87d12c3307 updated citation Heng Li 2018-05-30 11:15:28 -04:00
  • d7b61a039e updated citation Heng Li 2018-05-30 11:11:55 -04:00
  • 248158a3e1 Resolved #168: citing the manpage for cs Heng Li 2018-05-30 11:03:16 -04:00
  • 9f4309c376 r777: avoid skipping too many seeds Heng Li 2018-05-11 10:25:18 -04:00
  • 463f9309f9 Merge branch 'hot-fix' into fix-long-gap Heng Li 2018-05-11 10:13:19 -04:00
  • abe989e355 the previous fix on int overflow is incomplete Heng Li 2018-05-11 10:12:57 -04:00
  • 881b4ca3a2 r774: Merge branch 'hot-fix' into fix-long-gap Heng Li 2018-05-11 10:02:17 -04:00
  • 10c6dd2551 r773: fixed an integer overflow Heng Li 2018-05-11 10:01:23 -04:00
  • 7ec6721c44 r772: option -Y not working Heng Li 2018-05-11 10:00:11 -04:00
  • e61812ee55 reduced gap len to trigger bad seed filtering Heng Li 2018-05-01 16:17:21 -04:00
  • 734ac379bb r770: matching N bases not working properly (#155) Heng Li 2018-04-30 19:55:23 -04:00
  • 759f8e4ac9 r769: filter out seeds breaking long gaps Heng Li 2018-04-24 15:37:37 -04:00
  • aef7b0744c r768: shortened preset; added dv tag (#25) Heng Li 2018-04-24 12:48:54 -04:00
  • 39f836eac8 r767: don't crash when there is no "cg" (#153) Heng Li 2018-04-24 12:32:37 -04:00
  • cbeb86dad6 Merge remote-tracking branch 'origin/master' Heng Li 2018-04-10 09:12:26 -04:00
  • 372c90ceb5 r764: fixed incorrect inversion mapq (#148) Heng Li 2018-04-10 09:11:49 -04:00
  • 2e2e69107c Small bugfix for paftools.js apregier 2018-04-04 14:19:16 -05:00
  • ee4cd089f7 r763: fine control long join flank len (#128) Heng Li 2018-03-29 14:16:58 -04:00
  • d302ab2ad7 Updated the manpage to v2.10 Heng Li 2018-03-27 12:29:09 -04:00
  • 2d7ec75d50 Release minimap2-2.10 (r761) v2.10 Heng Li 2018-03-27 11:45:44 -04:00
  • 7938ed4893 fixed two mappy warnings Heng Li 2018-03-26 15:12:54 -04:00
  • 4740423afa Merge remote-tracking branch 'origin/master' Heng Li 2018-03-26 14:37:17 -04:00
  • 1776311a9b updated cookbook Heng Li 2018-03-26 14:37:02 -04:00
  • c1a3e05cb0 Merge pull request #138 from zingdle/patch-1 Heng Li 2018-03-26 07:50:39 -04:00
  • ecb6703d4a Update README.md zingdle 2018-03-26 14:54:52 +08:00
  • 0bf97a367b r755: junceval to only evaluate chromosomes Heng Li 2018-03-24 23:10:06 -04:00
  • 1c504d72e4 r754: option to only change name Heng Li 2018-03-23 12:27:11 -04:00
  • 5ef9580b17 r753: change bandwidth in ava-ont to 2000bp Heng Li 2018-03-23 10:15:23 -04:00
  • 08bd2123b6 r752: option to copy comments to output (#136) Heng Li 2018-03-23 10:04:33 -04:00
  • 8766d286df r751: optionally output MD (#118) Heng Li 2018-03-22 14:15:33 -04:00
  • 623b5d9d48 r750: check puts() return (#132 & #103) Heng Li 2018-03-22 11:31:58 -04:00
  • 18659118cd r749: don't print version etc at low verbose Heng Li 2018-03-22 11:10:55 -04:00
  • d1050f4eaf r748: optionally to use system getopt() (#134) Heng Li 2018-03-19 11:18:26 -04:00
  • b81d45510e Revision v2 Heng Li 2018-03-16 11:18:06 -04:00
  • d135feb1a5 response to reviewers' comments, round 2 Heng Li 2018-03-15 21:59:57 -04:00
  • 242ff4e91d r745: junceval - recognize "-" as file name Heng Li 2018-03-15 12:48:33 -04:00
  • 7a0c1316ce added more examples to cookbook Heng Li 2018-03-12 22:24:22 -04:00
  • 77ebd479f4 r743: added VCF output to "call" Heng Li 2018-03-12 21:51:31 -04:00
  • e3f226a9d9 working on section "Full-Genome Alignment" Heng Li 2018-03-12 16:12:18 -04:00
  • bdc615c1d4 r741: added --min-occ-floor to improve #107 Heng Li 2018-03-12 14:32:27 -04:00
  • ad1beaf255 backup; not finished Heng Li 2018-03-12 13:20:25 -04:00
  • de0480ac5b finished section "Read Overlap" Heng Li 2018-03-12 13:05:51 -04:00
  • f2866533a8 finished "mapping genomic reads" Heng Li 2018-03-12 12:50:21 -04:00
  • 0173850ef0 don't use bullets - they are hard to read Heng Li 2018-03-12 12:42:13 -04:00
  • acea3594fb updated cookbook Heng Li 2018-03-12 12:39:57 -04:00
  • f78a247749 Started to work on a cookbook Heng Li 2018-03-12 12:00:44 -04:00
  • ccaf12e1a2 r734: removed debugging print in call() Heng Li 2018-03-09 23:46:21 -05:00