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Author SHA1 Message Date
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) 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 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
Heng Li 83a8ee7038 r888: fixed incorrect CIGAR when --eqx in use 
This was caused by mm_fix_cigar() which may change query/target offset in very
rare cases. Generating EQX has to beware of this change.

Resolves #266
 2018-11-18 14:22:29 -05:00
Heng Li 62bbadf668 r887: fixed a bug in asmgene 2018-11-11 21:35:19 -05:00
Heng Li 91f548b497 r886: fixed two minor typos 
Resolves #264
Resolves #265
 2018-11-08 12:04:14 -05:00
Heng Li cdaf46665a r885: compute dup with asmstat 2018-11-07 00:26:05 -05:00
Heng Li 6596c63dcd r884: for C++ compatibility (#261) 2018-11-06 22:07:11 -05:00
Heng Li 59f23f7579 Release minimap2-2.14 (r883) 2018-11-06 00:03:16 -05:00
Heng Li 5e55e397e9 r882: guard against -E0 (#263) 2018-11-05 23:36:12 -05:00
Heng Li 88c421e8de r881: a recent change reduces sr accuracy 2018-11-05 22:03:59 -05:00
Heng Li 3db5bfe6e5 r880: fixed false wrong FASTA/Q alert 2018-11-05 20:52:07 -05:00
Heng Li 83dfdd5f50 draft release note 2018-11-05 20:07:57 -05:00
Heng Li 8a2b1cd4c9 updated mappy for extra option max_sw_mat 2018-11-05 19:28:44 -05:00
Heng Li 1ede8ca170 r877: renamed cap-sw-mat to cap-sw-mem 2018-11-05 11:46:38 -05:00
Heng Li 13981404e2 r876: skip DP if taking too much RAM (#259) 2018-11-05 11:43:10 -05:00
Heng Li fd64dd26f6 r875: warn given incorrect FASTA/Q 
resolves #252
resolves #255
 2018-11-05 10:02:44 -05:00
Heng Li 24df95e4b8 r874: don't call x86_simd() so often 
This takes a few percent of time in profiler.
 2018-11-05 09:20:35 -05:00
Heng Li a8ee48c2ce r873: comforming to C99/C11; resolves #261 2018-11-05 08:25:07 -05:00
Heng Li 09e089c3dc r872: choose the longest isoform 2018-11-04 23:48:50 -05:00
Heng Li e46cbb7d84 r871: print erroneous genes 2018-11-04 20:37:06 -05:00
Heng Li 57ec73ec6c r870: separate <50% and <10% 2018-11-04 19:31:25 -05:00
Heng Li 9e27575387 r869: classify incomplete genes 2018-11-04 19:21:55 -05:00
Heng Li b4ad8d8bf0 added asmgene 
improvements coming; not made public yet
 2018-11-04 17:24:05 -05:00
Heng Li e315b9fada hidden options to control bp calculation 2018-11-04 16:36:04 -05:00
Heng Li 42baf287a4 r866: fixed a typo; resolves #262 2018-10-30 09:11:55 -04:00
Heng Li 2ceba22a7a fixed a typo in manpage 2018-10-28 11:51:02 -04:00
Heng Li 9ed56b4a25 r860: MD/cs not working with --eqx 2018-10-26 23:23:53 -04:00
Heng Li ecb6c5c36c Document --no-pairing (#256) 2018-10-23 10:00:21 -04:00
Heng Li 377c7099a8 r858: fixed a bug; resolves #254 2018-10-22 22:47:11 -04:00
Heng Li 51e2abfa60 clarify that minimap2 may miss small exons 2018-10-22 11:16:16 -04:00
Heng Li 7b0a49732e r856: wrongly reported for an unrecognized option 
Resolved #250
 2018-10-19 20:07:14 -04:00
Heng Li 20268a6068 updated the copyright holder 2018-10-18 11:11:17 -04:00
Heng Li d04ac068fd r852: a minor when large --end-bonus is in use 
We may use a large --end-bonus to mimic end-to-end alignment. In the short-read
mode, the candidate alignment region may be out of the band, which leads to
truncated alignment.
 2018-10-15 21:28:27 -04:00
Heng Li 5d5d392c02 Release minimap2-2.13 (r850) 2018-10-11 13:18:31 -04:00
Heng Li 170863e553 r849: option -P doesn't work 
I don't know why I haven't found it at the beginning.
 2018-10-04 16:11:59 -04:00
Heng Li 97f97306a4 r847: guard against -N0 2018-09-27 15:13:44 -04:00
Heng Li 1077b7ddc8 r846: added --hard-mask-level for #244 2018-09-27 14:46:26 -04:00
Heng Li c57b59f02f r845: log peak memory 2018-09-23 20:27:49 -04:00
Heng Li 8b12da8b0f removed a useless dependency (not in repo) 2018-09-17 13:59:25 -04:00
Heng Li c63a33904f r836: fixed an integer overflow 
Forgot this one.
 2018-09-14 23:29:31 -04:00
Heng Li 70b0fede64 r835: improved help message. Resolved #232 2018-09-14 22:29:25 -04:00
Heng Li 0b681e51e7 Merge remote-tracking branch 'remotes/origin/master' 2018-09-14 22:22:20 -04:00
Heng Li 7d80d6de4a r832: fixed outdated -L. Resolved #231 and #233 2018-09-14 22:21:33 -04:00
Heng Li 98c48a1c45 Fixed wrong version links in the cookbook 2018-09-03 09:07:34 -04:00
Heng Li 63d397120a removed getopt.c from MANIFEST 2018-09-01 21:30:46 -04:00
Heng Li 7998fe9906 r829: replaced musl's getopt with ketopt 2018-09-01 21:18:02 -04:00
Heng Li 3a119d606f r828: --MD to support spliced alignment 2018-08-22 10:47:45 -04:00
Heng Li a5eafb75f9 Release minimap2-2.12 (r827) 2018-08-06 12:44:39 -04:00
Heng Li 9a567e4b37 allow mappy to change scoring 2018-08-06 09:52:13 -04:00
Heng Li 8e606bcc06 added a -C5 example to Getting Started 2018-08-06 09:08:33 -04:00
Heng Li a1b7219b5d explain added parameters 2018-08-05 21:32:05 -04:00
Heng Li b0f39a1a61 r823: mappy to index a single sequence 2018-08-05 20:57:05 -04:00
Heng Li 5ab6538757 r822: added option --no-end-flt 2018-08-05 19:42:12 -04:00
Heng Li b32296e18f r821: fixed memory when -y is used 2018-07-31 15:14:37 -04:00
Heng Li 99ecdf7b5d mappy to support arm64 (#203) 2018-07-24 23:53:02 -04:00
Heng Li ff9917a1c4 r819: mappy to support cs/MD 2018-07-24 23:29:55 -04:00
Heng Li 0e137670fc Merge branch 'split' 2018-07-15 22:24:15 -04:00
Heng Li 395c8d678a r815: fixed a memory leak 2018-07-15 22:11:32 -04:00
Heng Li 830da7fa27 r814: resumed versioning 2018-07-15 11:48:14 -04:00
Heng Li a655cbef86 print SAM header; remove tmp files 2018-07-15 11:03:18 -04:00
Heng Li 4b707aac92 working with toy examples 2018-07-15 10:55:00 -04:00
Heng Li 951c0d1d35 apparently mm_append_cigar() wastes some memory 2018-07-14 23:47:44 -04:00
Heng Li 3545e35a42 pairing in the split-idx mode 2018-07-14 23:43:34 -04:00
Heng Li f3417da838 bugfix: unmapped records are duplicated in output 2018-07-14 22:54:05 -04:00
Heng Li e5277dbf5c code backup 2018-07-14 22:52:36 -04:00
Heng Li 1a55227d5a write hits to tmp files (unfinished) 2018-07-14 12:15:10 -04:00
Heng Li 5cfa621b2d use unmapped records 2018-07-07 12:49:15 -05:00
Heng Li a609a07f8c optionally output unmapped query in PAF 2018-07-07 10:26:08 -05:00
Heng Li bcf92b3c46 compute query coverage 2018-07-06 21:52:01 -05:00
Heng Li 097378ab90 reworked break point counting 2018-07-06 09:46:26 -04:00
Heng Li 10bbbe28c5 added asmstat 2018-07-05 13:22:32 -04:00
Heng Li 50dae10421 paftools call to show statistics on longer indels 2018-07-03 14:28:09 -04:00
Heng Li 0517972d02 Release minimap2-2.11 (r797) 2018-06-21 00:04:08 -04:00
Heng Li d46e68e6ad r796: don't use ssize_t 2018-06-20 12:45:27 -04:00
Heng Li 2584a4149a r295: use -r2000 for ava-ont, NOT for ava-pb 2018-06-20 12:24:43 -04:00
Heng Li 66674afd09 r794: fixed a bug in seed filtering 2018-06-20 10:26:29 -04:00
Heng Li e9ca0c9dab added __version__; resolved #165 
Not sure if this is the right way. Apparently working.
 2018-06-19 15:40:26 -04:00
Heng Li 7e6e8ca73f r792: fixed -Wextra warnings and resolved #184 2018-06-19 15:26:58 -04:00
Heng Li 154d2caf5b r784: support the =/X CIGAR operators (#156) 2018-05-30 16:11:22 -04:00
Heng Li a3afeec0b2 r783: reverted to r781 (#155) 2018-05-30 15:25:34 -04:00
Heng Li 3573784b4d r782: no mask a chain having long ref ovlp (#155) 2018-05-30 13:53:45 -04:00
Heng Li 872f300955 r781: fixed the buggy heapmerge (resolves #166) 2018-05-30 11:55:14 -04:00
Heng Li d7b61a039e updated citation 2018-05-30 11:11:55 -04:00
Heng Li 248158a3e1 Resolved #168: citing the manpage for cs 2018-05-30 11:03:16 -04:00
Heng Li 9f4309c376 r777: avoid skipping too many seeds 2018-05-11 10:25:18 -04:00
Heng Li 463f9309f9 Merge branch 'hot-fix' into fix-long-gap 2018-05-11 10:13:19 -04:00
Heng Li abe989e355 the previous fix on int overflow is incomplete 2018-05-11 10:12:57 -04:00
Heng Li 881b4ca3a2 r774: Merge branch 'hot-fix' into fix-long-gap 2018-05-11 10:02:17 -04:00
Heng Li 10c6dd2551 r773: fixed an integer overflow 2018-05-11 10:01:23 -04:00