zzh
/
minimap2
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity
1,102 Commits
1 Branch
0 Tags
1.7 MiB
Commit Graph

1102 Commits (1641a66d1503936b6881c586078eb21065b680a7)

Author SHA1 Message Date
Heng Li 5f449c5cae fixed potential integer overflows 2021-07-16 17:20:05 -04:00
Heng Li b046052d82 Merge branch 'master' into utec 2021-07-16 13:32:47 -04:00
Jason Stajich 5cc3d2239f missing target object files from Makefile.simde to fix issue #779 2021-07-07 23:07:27 -04:00
Heng Li 581f2d7123 Release minimap2-2.21 (r1071) 2021-07-06 13:18:55 -04:00
Heng Li 52dbd439bc r1080: re-versioning 2021-07-02 20:26:13 -04:00
John Marshall 260a68d232 Use #defines for CIGAR operators in C code 
Give the CIGAR constants names to clarify the code. So that ksw2.h
remains self-contained, define KSW_* versions of the CIGAR operators
it needs for use within ksw2.h. Other code should in general use the
full set of MM_CIGAR_* constants in minimap.h.
 2021-07-02 13:03:03 -04:00
John Marshall 177eef259d Use the full MIDNSHP=X string whenever printing CIGAR strings 
Define MM_CIGAR_STR to the full string of CIGAR operators (including
the 'B' operator as well) and use it throughout the C code.

It would be possible to use it from the Cython code too, but it's easier
to keep that as a Cython string literal to avoid adding extra runtime
code to handle locale conversion.
 2021-07-02 13:03:03 -04:00
Heng Li 459ce04c84 r1069: fixed a regression in comparison to v2.18 
for PE short reads. An interesting omission. Resolves #776
 2021-07-02 11:45:21 -04:00
Heng Li e6cce019e4 r1068: fixed a bug caused by 3f71478 
Resolves #752 (again)
 2021-06-30 19:20:06 -04:00
Heng Li 7025b0b941 Merge branch 'master' of github.com:lh3/minimap2 2021-06-16 10:18:40 -04:00
Heng Li fe6a0bb337 r1064: fixed another uninitialized condition 
This one should also be harmless. It affects a min value, but that value is not
actually used.
 2021-06-16 10:16:36 -04:00
Heng Li 3f7147864b r1063: fixed an uninitialized access (#752) 
This one is harmless.
 2021-06-16 09:27:30 -04:00
Torsten Houwaart c83589b9ea Update README.md 
Clarification on approximate mapping
 2021-06-10 09:36:39 -04:00
Heng Li ce7a59f412 Fixed a typo in README 
I just hate my butterfly keyboard!
 2021-05-27 15:43:04 -04:00
Heng Li 15471bd629 Release minimap2-2.20 (r1061) 2021-05-27 15:26:04 -04:00
Heng Li ca19463268 r1060: safer ways to use -rNUM1,NUM2 2021-05-27 10:55:13 -04:00
Heng Li 4f8d1bc360 r1059: with --rmq, use the larger bandwidth 2021-05-26 23:01:49 -04:00
Heng Li 1776c0c645 missing seed.c in setup.py 
Ok, I am not going to re-release again...
 2021-05-26 21:36:09 -04:00
Heng Li 9febf532c1 Release minimap2-2.19 (r1057) 2021-05-26 21:23:42 -04:00
Heng Li cec23131e4 fixed a python compilation error 
Caused by chain.c -> lchain.c
 2021-05-26 21:20:48 -04:00
Heng Li ef09ccf104 Release minimap2-2.19 (r1055) 2021-05-26 21:01:03 -04:00
Heng Li e74dfd1aa9 r1054: fixed a memory leak 2021-05-26 12:32:04 -04:00
Heng Li f31705bb4a r1053: made junceval work with PAF 2021-05-26 11:54:46 -04:00
Heng Li 41d7ccb191 r1052: default -g to 5k 2021-05-24 16:46:16 -04:00
Heng Li 34a41197d7 r1051: added two internal parameters 
rmq_rescue_size and rmq_rescue_ratio
 2021-05-24 16:38:45 -04:00
Heng Li 9626b3e716 r1050: -r accepts two bandwidths 2021-05-24 16:29:21 -04:00
Heng Li 379728726a r1049: removed the long-join heuristics 2021-05-24 16:21:40 -04:00
Heng Li 4f91558160 r1048: rescue long gaps 2021-05-24 16:09:09 -04:00
Heng Li ec3bc6efd7 r1047: make gap penalty proportional to k-mer 
closer to the older minimap2
 2021-05-24 13:18:17 -04:00
Heng Li 8ec8866100 Merge branch 'master' into dev-rmq 2021-05-23 21:01:04 -04:00
Heng Li 9e7247cff9 sync python with recent changes 2021-05-23 21:00:15 -04:00
Ariel Erijman cd66777bfb small typo 2021-05-23 13:09:55 -04:00
Heng Li 5d7d25e92d Merge remote-tracking branch 'origin/master' 2021-05-23 13:08:52 -04:00
Heng Li 2a3793bbd2 clarify that map-hifi is for HEAD only 
Resolves #747
 2021-05-23 13:08:15 -04:00
Heng Li f97008a10e Merge branch 'master' into dev-rmq 2021-05-20 19:36:33 -04:00
Cornelius Roemer 10502e2a78 Fixed typo in Readme.md 
deltion -> deletion
 2021-05-14 15:38:30 -04:00
Don Kirkby 4422c0c6f9 Typo fix in Python README. 
Thanks for sharing minimap2. Here's a little fix.
 2021-05-14 15:38:12 -04:00
Heng Li 42a11e1d58 Changed Travis to Github Actions in README 2021-05-10 12:58:25 -04:00
Heng Li 76df351fa8 added github action 2021-05-10 12:55:58 -04:00
Heng Li d065d3bead Merge branch 'master' into dev-rmq 2021-05-10 12:42:57 -04:00
Heng Li ac146fe7bc r1035: failed to index under the --frag=yes mode 
Resolves #734
 2021-05-10 12:36:48 -04:00
Heng Li 6c96078ed0 r1034: changed multiple defaults; updated manpage 2021-05-03 22:51:34 -04:00
Heng Li bbb4f97e52 support RMQ 2021-05-03 09:27:04 -04:00
Heng Li b7f4d8a0f4 removed the old minimap2 chaining 2021-05-02 18:55:37 -04:00
Heng Li e81927e7a1 prepare to backport unimap/minigraph chaining 2021-05-02 18:25:49 -04:00
Heng Li f7dc5799c5 clarify CLR when necessary 2021-05-01 15:56:33 -04:00
Heng Li 817cb81cb0 Updated README for the HiFi preset 2021-05-01 15:47:25 -04:00
Heng Li 0f5608c4a4 r1028: backport minigraph -U 2021-05-01 15:41:39 -04:00
Heng Li e8823a3709 r1027: renamed hifi to map-hifi; changed default 2021-05-01 15:22:51 -04:00
Heng Li 7edeec67b0 r1026: fixed bugs in seed sampling add hifi 2021-05-01 15:07:56 -04:00