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  • 77ebd479f4 r743: added VCF output to "call" Heng Li 2018-03-12 21:51:31 -0400
  • e3f226a9d9 working on section "Full-Genome Alignment" Heng Li 2018-03-12 16:12:18 -0400
  • bdc615c1d4 r741: added --min-occ-floor to improve #107 Heng Li 2018-03-12 14:32:27 -0400
  • ad1beaf255 backup; not finished Heng Li 2018-03-12 13:20:25 -0400
  • de0480ac5b finished section "Read Overlap" Heng Li 2018-03-12 13:05:51 -0400
  • f2866533a8 finished "mapping genomic reads" Heng Li 2018-03-12 12:50:21 -0400
  • 0173850ef0 don't use bullets - they are hard to read Heng Li 2018-03-12 12:42:13 -0400
  • acea3594fb updated cookbook Heng Li 2018-03-12 12:39:57 -0400
  • f78a247749 Started to work on a cookbook Heng Li 2018-03-12 12:00:44 -0400
  • ccaf12e1a2 r734: removed debugging print in call() Heng Li 2018-03-09 23:46:21 -0500
  • 96b132c97d fixed a bug/typo in Aligner.seq() (#126) Heng Li 2018-03-08 19:12:12 -0500
  • 70428ca3a8 speedup tag parsing for sam2paf Heng Li 2018-03-02 10:17:55 -0500
  • 9aea79d621 faster tag parsing Heng Li 2018-03-02 10:09:14 -0500
  • 1770988627 make calling work with sam2paf output Heng Li 2018-03-02 10:03:06 -0500
  • 2bfdad34bb minor cleanup to last commit Heng Li 2018-03-02 01:07:37 -0500
  • 953766cedd generate cs; not carefully tested Heng Li 2018-03-02 00:14:55 -0500
  • dc61301d9f sam2paf cleanup Heng Li 2018-03-01 21:58:12 -0500
  • 19e05a099d for clarity Heng Li 2018-03-01 18:25:29 -0500
  • 0238caa8b1 clarify minimap2 not working for >2Gbp seq #129 Heng Li 2018-03-01 18:23:40 -0500
  • a22ebb9836 use SSE compiler flags more precisely (#127) Heng Li 2018-02-26 09:51:01 -0500
  • eeb314edd6 Release minimap2-2.9 (r720) Heng Li 2018-02-24 09:31:09 -0500
  • 83c57a9d98 r719: fixed bad memory access Heng Li 2018-02-23 17:27:41 -0500
  • 24a4808826 r718: retrieve sequence from the index Heng Li 2018-02-23 10:18:26 -0500
  • 29ed675ee5 bugfix: in-place revcomp() not working Heng Li 2018-02-20 11:05:54 -0500
  • 7dc7097208 added reverse complement Heng Li 2018-02-20 09:41:25 -0500
  • f434653432 added peakrss(); not used for now Heng Li 2018-02-17 20:40:31 -0500
  • 090361c25b fixed a typo in mappy (#117) Heng Li 2018-02-16 21:10:57 -0500
  • e1f18690f6 paftools-r713: fixed bug for cov1 regions Heng Li 2018-02-16 12:20:46 -0500
  • 54a42aafe5 keep documents in sync Heng Li 2018-02-15 17:21:09 -0500
  • 8fc5f8dc90 r711: assign proper mapq to primary inversions Heng Li 2018-02-15 14:34:59 -0500
  • a0d62519c1 r710: fixed incorrect inversion coordinate (#112) Heng Li 2018-02-15 14:23:42 -0500
  • b71c01b316 added test data for inversions Heng Li 2018-02-15 11:04:27 -0500
  • 1372977a37 r708: implemented double Z-drop thresholds (#112) Heng Li 2018-02-14 17:10:02 -0500
  • c0e0d5d84b r707: bugfix for inversions on rev strand (#112) Heng Li 2018-02-14 14:09:03 -0500
  • b328795051 r706: don't segfault upon wrong FASTA/Q (#111) Heng Li 2018-02-13 10:00:22 -0500
  • 3b17d62ccd minor doc improvements Heng Li 2018-02-12 22:27:02 -0500
  • 874b8c4795 rework misc/README; progressing but unfinished Heng Li 2018-02-12 22:06:05 -0500
  • 7ef5490884 r703: added --max-clip-ratio Heng Li 2018-02-12 13:29:18 -0500
  • f66de7df59 updated paftools revision number to r702 Heng Li 2018-02-12 11:39:04 -0500
  • fbbd4e0968 changed output messages for clarity Heng Li 2018-02-12 11:32:32 -0500
  • 8c89ba005e merged cnt-feat into paftools Heng Li 2018-02-12 11:29:42 -0500
  • 50775a1e6f added liftOver Heng Li 2018-02-12 11:12:23 -0500
  • 87cf650168 r697: fixed wrong #mapped reads in junceval Heng Li 2018-02-09 18:45:57 -0500
  • 6e65c5e631 Revision 1 Heng Li 2018-02-09 17:39:02 -0500
  • a58b05a61b extend the section on genome alignment Heng Li 2018-02-09 13:59:00 -0500
  • 42dab6319b don't call SNPs involving 'n' Heng Li 2018-02-09 13:27:17 -0500
  • 8428809369 convert MUMmer's delta to PAF Heng Li 2018-02-09 12:14:28 -0500
  • 642af5591e merged intron-eval into paftools Heng Li 2018-02-09 11:07:14 -0500
  • 2025a6279a merged gff2bed and mapstat to paftools Heng Li 2018-02-09 10:47:12 -0500
  • 3465b04724 merged a few converters to paftools Heng Li 2018-02-09 10:23:30 -0500
  • 66c5e71fa8 merging scripts into one long script Heng Li 2018-02-09 10:00:35 -0500
  • 01560f1db0 Revision v1, to be submitted Heng Li 2018-02-07 11:07:08 -0500
  • 39535565ee first round of revision Heng Li 2018-02-06 16:19:22 -0500
  • a8d476c6ad r686: end seed trimming don't go over long join Heng Li 2018-02-06 11:31:32 -0500
  • 29b4a1786c r685: tune end seed filter again Heng Li 2018-02-05 11:48:22 -0500
  • dbf284b2d9 r684: separate end score from min_chain_score Heng Li 2018-02-05 11:40:38 -0500
  • 3df5015668 General doc improvements Heng Li 2018-02-02 21:45:46 -0500
  • 756379bf83 Documented paf2diff.js (more to come later) Heng Li 2018-02-02 14:43:58 -0500
  • 41fd8a966a Documented ov-eval.js Heng Li 2018-02-02 14:18:18 -0500
  • 86e4933b1a Added TOC Heng Li 2018-02-02 14:12:30 -0500
  • a633a744b6 more doc in misc Heng Li 2018-02-02 14:07:17 -0500
  • ddc31f57ba Documented some k8 scripts; more coming Heng Li 2018-02-02 13:57:08 -0500
  • 35d3e064bf r677: reduce the change of missing hits Heng Li 2018-02-02 10:35:33 -0500
  • 997ab9bb2e Fixed the description of --dual Heng Li 2018-02-01 15:11:51 -0500
  • 53ce317e59 Release minimap2-2.8 (r672) Heng Li 2018-02-01 12:27:15 -0500
  • da6947cfa3 r671: cleanup command line options Heng Li 2018-01-31 13:59:52 -0500
  • 46d6349af4 r670: added PE support to mappy Heng Li 2018-01-31 11:33:08 -0500
  • 12a5a5fa3c r669: improved self chain extension (#10) Heng Li 2018-01-30 20:05:02 -0500
  • ad18fa490d fixed typos Heng Li 2018-01-30 10:11:50 -0500
  • 43bfa6199d r667: warn if one query file has fewer records #92 Heng Li 2018-01-28 17:36:21 -0500
  • 72b9b0e3b6 r666: report if >=3 query files in SR mode #92 Heng Li 2018-01-28 17:15:57 -0500
  • 6205fa6f21 document --heap-sort Heng Li 2018-01-26 15:15:40 -0500
  • d676a5314b r664: use --heat-sort for sr by default Heng Li 2018-01-26 12:25:42 -0500
  • dfc78b39d3 refactor the old sorting Heng Li 2018-01-26 09:37:48 -0500
  • 7b57c9a619 heap sort working on MT Heng Li 2018-01-26 09:21:45 -0500
  • 123bc1d91d put option operations in another file Heng Li 2018-01-26 08:38:37 -0500
  • dd18307e66 code backup Heng Li 2018-01-25 21:52:49 -0500
  • 543fa12e68 r659: for C++ compatibility Heng Li 2018-01-19 10:40:18 -0500
  • af1a871270 r658: gives a warning if -N0 is used Heng Li 2018-01-19 08:33:20 -0500
  • 2b71181a37 r657: check -p (#96) Heng Li 2018-01-19 01:03:38 -0500
  • 0454e6be91 explain -M in the manpage Heng Li 2018-01-18 11:47:11 -0500
  • 33f8157961 r655: options to map to one strand of the ref #91 Heng Li 2018-01-16 10:34:30 -0500
  • eecc06086f Released minimap2-2.7 (r654) Heng Li 2018-01-09 13:16:00 -0500
  • dfea113f28 r653: the last change may write "N" wrongly Heng Li 2018-01-08 11:33:53 -0500
  • 1842d7f5b5 allow to exclude regions Heng Li 2018-01-07 22:35:56 -0500
  • f5cfd439ee r651: incorrectly treat introns as deletions Heng Li 2018-01-07 19:42:50 -0500
  • 248b43cc47 work with targets in BED12 Heng Li 2018-01-07 19:39:25 -0500
  • bf72969ab1 added a bed counter Heng Li 2018-01-07 15:19:18 -0500
  • 7b5a601d48 support paired-end reads Heng Li 2018-01-07 13:53:26 -0500
  • 405d531100 don't test python v3.3 Heng Li 2018-01-05 22:17:00 -0500
  • e9607fcd9b allow to convert read names Heng Li 2018-01-05 22:05:15 -0500
  • a465a920ec bug in block starts; added color and short-name Heng Li 2018-01-05 21:45:56 -0500
  • b20839be77 more robust ID conversion Heng Li 2018-01-05 17:55:24 -0500
  • 209beb9955 convert EnsEMBL to UCSC name (optional) Heng Li 2018-01-05 17:41:18 -0500
  • cfe87f50c1 convert GTF/GFF3 to BED12 Heng Li 2018-01-05 17:10:43 -0500
  • 680b971bb0 deleted duplicated entries Heng Li 2018-01-01 19:52:21 -0500
  • 6b0d3c1fa8 added PHONY and comments to makefile Heng Li 2017-12-30 20:54:11 -0500
  • dc9e3dcf4a r639: changed -O/-E validation Heng Li 2017-12-30 20:39:29 -0500
  • cc75c12905 r638: disabled scoring checking Heng Li 2017-12-30 07:50:40 -0500
  • f159e1c2d3 new section on HPC k-mers Heng Li 2017-12-24 19:11:23 -0500