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60 Commits

Author SHA1 Message Date
Heng Li
9bb4d2bed4 r1290: support ds in Python 2025-12-12 11:39:01 -05:00
Heng Li
1877818239 r1255: moved jump code to a separate file 2025-04-06 09:33:51 -04:00
Heng Li
f1b3c7ad06 added -ldl for asan on some linux 2023-04-25 11:14:15 -04:00
Heng Li
c2f07ff2ac r1149: implemented random open syncmer 
On the mm2-update dataset, -j8 leads to sparser k-mer selection at higher
accuracy. The speed becomes a little slower. There seems a benefit but not a
big one.
 2022-10-21 19:07:28 -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
feb92d32ea r1025: seed rescuring 2021-04-30 17:33:16 -04:00
Heng Li
ccb0f7b05d added a new Makefile for simde 2020-04-25 22:43:29 -04:00
mbrcic
2b3403f094 fix for Neon after test. 2020-04-21 02:08:21 +02:00
mbrcic
f47e8a525e SIMDe made optional. Include paths changes for SIMDe. 2020-04-21 01:08:32 +02:00
mbrcic
c172df7d2d fix for Neon 2020-04-20 21:14:15 +02:00
mbrcic
9e6fdd376b Changed sse2neon with SIMDe. Added building non-SIMD version. 2020-04-20 18:28:06 +02:00
Heng Li
367aed4271 added the asan and tsan targets to Makefile 2019-12-23 17:33:10 -05:00
Heng Li
8b12da8b0f removed a useless dependency (not in repo) 2018-09-17 13:59:25 -04:00
Heng Li
7998fe9906 r829: replaced musl's getopt with ketopt 2018-09-01 21:18:02 -04:00
Heng Li
1a55227d5a write hits to tmp files (unfinished) 2018-07-14 12:15:10 -04:00
Heng Li
66674afd09 r794: fixed a bug in seed filtering 2018-06-20 10:26:29 -04:00
Heng Li
7e6e8ca73f r792: fixed -Wextra warnings and resolved #184 2018-06-19 15:26:58 -04:00
Hasindu Gamaarachchi
99dcd75f64 added support for 64 bit ARM architectures 2018-06-19 14:28:45 -04:00
Heng Li
a22ebb9836 use SSE compiler flags more precisely (#127) 2018-02-26 09:51:01 -05:00
Heng Li
53ce317e59 Release minimap2-2.8 (r672) 2018-02-01 12:50:20 -05:00
Heng Li
123bc1d91d put option operations in another file 2018-01-26 08:38:37 -05:00
Heng Li
6b0d3c1fa8 added PHONY and comments to makefile 2017-12-30 20:54:11 -05:00
Hasindu Gamaarachchi
8995e2e078 added support for arm neon 2017-12-15 17:42:19 +11:00
Heng Li
ae85dcde76 added esterr.o dependencies 2017-12-13 09:01:48 -05:00
Heng Li
704ff9f4c6 r607: estimate sequence divergence 
Currently using the simplest method. There may be a more accurate estimate.
 2017-12-06 16:14:39 -05:00
Heng Li
e0baf1ad54 r479: a bit code cleanup 2017-10-05 16:15:14 -04:00
Heng Li
55d1e4f638 r440: better chain filtering for PE reads 2017-09-26 11:03:36 -04:00
Heng Li
e9e86f5a48 try python build again 2017-09-17 00:46:39 -04:00
Heng Li
d5012a1b17 this is embarrassing: rename again to mappy 2017-09-17 00:05:30 -04:00
Heng Li
28fd3d63fd renamed module name from minimap2 to mmappy 
minimap2 clashed with minimap2 from conda
 2017-09-16 23:29:41 -04:00
Heng Li
10bd4079d1 fixed a bug on rev strand; added example 2017-09-16 17:51:13 -04:00
Heng Li
7e34bea7ab minor 2017-09-16 09:30:00 -04:00
Heng Li
46e8b6a4f9 r338: portable CPU dispatch, which is the default 
working with gcc, icc, clang and msvc.
 2017-09-03 20:29:24 -04:00
Heng Li
3c997ca016 r337: support CPU dispatch for gcc-4.8+ 
using __builtin_cpu_supports()
 2017-09-03 14:29:49 -04:00
Heng Li
0a3ebdc916 for better windows compatibility 2017-09-02 17:52:33 -04:00
Heng Li
eccdb3a1ca r315: added getopt from musl 2017-09-01 20:20:34 +08:00
Heng Li
61eef0575c separate out spliced alignment; not right yet 2017-08-12 18:54:32 -04:00
Heng Li
163fa36ee6 r281: don't open long gaps on query 2017-08-10 15:04:59 -04:00
Heng Li
5934d68772 r229: a new way to prevent out-of-band backtrack 2017-07-29 23:52:30 -04:00
Heng Li
d08b7a0c51 r227: use local alignment for INV alignment 2017-07-29 17:40:53 -04:00
Heng Li
947cf162be update dependency; delete minimap2-lite on clean 2017-07-18 14:48:46 -04:00
Heng Li
293a7049f3 migrated minimap/example.c here. 2017-07-18 14:43:43 -04:00
Heng Li
a1addb2949 use -msse4 by default, not -march 2017-07-18 13:56:51 -04:00
Heng Li
cc554aee43 r159: use two-piece gap penalty 2017-07-08 10:26:00 -04:00
Heng Li
2e4fd9f1d0 r148: revamped regs handling after cigar 2017-07-03 10:44:26 -04:00
Heng Li
ecedfe5788 code refactoring for mm_reg1_t 2017-06-29 19:35:38 -04:00
Heng Li
17944a75c2 merge into map.c 2017-06-29 14:20:14 -04:00
Heng Li
d274e1b743 backup 2017-06-29 12:58:52 -04:00
Heng Li
cf703655cb optional sse4 2017-06-28 22:21:52 -04:00