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
b7f4d8a0f4
removed the old minimap2 chaining
2021-05-02 18:55:37 -04:00
e81927e7a1
prepare to backport unimap/minigraph chaining
2021-05-02 18:25:49 -04:00
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
ccb0f7b05d
added a new Makefile for simde
2020-04-25 22:43:29 -04:00
2b3403f094
fix for Neon after test.
2020-04-21 02:08:21 +02:00
f47e8a525e
SIMDe made optional. Include paths changes for SIMDe.
2020-04-21 01:08:32 +02:00
c172df7d2d
fix for Neon
2020-04-20 21:14:15 +02:00
9e6fdd376b
Changed sse2neon with SIMDe. Added building non-SIMD version.
2020-04-20 18:28:06 +02:00
367aed4271
added the asan and tsan targets to Makefile
2019-12-23 17:33:10 -05:00
8b12da8b0f
removed a useless dependency (not in repo)
2018-09-17 13:59:25 -04:00
7998fe9906
r829: replaced musl's getopt with ketopt
2018-09-01 21:18:02 -04:00
1a55227d5a
write hits to tmp files (unfinished)
2018-07-14 12:15:10 -04:00
66674afd09
r794: fixed a bug in seed filtering
2018-06-20 10:26:29 -04:00
7e6e8ca73f
r792: fixed -Wextra warnings and resolved #184
2018-06-19 15:26:58 -04:00
99dcd75f64
added support for 64 bit ARM architectures
2018-06-19 14:28:45 -04:00
a22ebb9836
use SSE compiler flags more precisely ( #127 )
2018-02-26 09:51:01 -05:00
53ce317e59
Release minimap2-2.8 (r672)
2018-02-01 12:50:20 -05:00
123bc1d91d
put option operations in another file
2018-01-26 08:38:37 -05:00
6b0d3c1fa8
added PHONY and comments to makefile
2017-12-30 20:54:11 -05:00
8995e2e078
added support for arm neon
2017-12-15 17:42:19 +11:00
ae85dcde76
added esterr.o dependencies
2017-12-13 09:01:48 -05:00
704ff9f4c6
r607: estimate sequence divergence
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Currently using the simplest method. There may be a more accurate estimate.
2017-12-06 16:14:39 -05:00
e0baf1ad54
r479: a bit code cleanup
2017-10-05 16:15:14 -04:00
55d1e4f638
r440: better chain filtering for PE reads
2017-09-26 11:03:36 -04:00
e9e86f5a48
try python build again
2017-09-17 00:46:39 -04:00
d5012a1b17
this is embarrassing: rename again to mappy
2017-09-17 00:05:30 -04:00
28fd3d63fd
renamed module name from minimap2 to mmappy
...
minimap2 clashed with minimap2 from conda
2017-09-16 23:29:41 -04:00
10bd4079d1
fixed a bug on rev strand; added example
2017-09-16 17:51:13 -04:00
7e34bea7ab
minor
2017-09-16 09:30:00 -04:00
46e8b6a4f9
r338: portable CPU dispatch, which is the default
...
working with gcc, icc, clang and msvc.
2017-09-03 20:29:24 -04:00
3c997ca016
r337: support CPU dispatch for gcc-4.8+
...
using __builtin_cpu_supports()
2017-09-03 14:29:49 -04:00
0a3ebdc916
for better windows compatibility
2017-09-02 17:52:33 -04:00
eccdb3a1ca
r315: added getopt from musl
2017-09-01 20:20:34 +08:00
61eef0575c
separate out spliced alignment; not right yet
2017-08-12 18:54:32 -04:00
163fa36ee6
r281: don't open long gaps on query
2017-08-10 15:04:59 -04:00
5934d68772
r229: a new way to prevent out-of-band backtrack
2017-07-29 23:52:30 -04:00
d08b7a0c51
r227: use local alignment for INV alignment
2017-07-29 17:40:53 -04:00
947cf162be
update dependency; delete minimap2-lite on clean
2017-07-18 14:48:46 -04:00
293a7049f3
migrated minimap/example.c here.
2017-07-18 14:43:43 -04:00
a1addb2949
use -msse4 by default, not -march
2017-07-18 13:56:51 -04:00
cc554aee43
r159: use two-piece gap penalty
2017-07-08 10:26:00 -04:00
2e4fd9f1d0
r148: revamped regs handling after cigar
2017-07-03 10:44:26 -04:00
ecedfe5788
code refactoring for mm_reg1_t
2017-06-29 19:35:38 -04:00
17944a75c2
merge into map.c
2017-06-29 14:20:14 -04:00
d274e1b743
backup
2017-06-29 12:58:52 -04:00
cf703655cb
optional sse4
2017-06-28 22:21:52 -04:00
b56cd790f6
enabled kalloc (was a mistake)
...
Not using kalloc leads to significant malloc overhead.
2017-06-26 15:41:55 -04:00
39083be9ab
separated formating printing
...
for SAM in future; and for performance
2017-06-25 16:13:54 -04:00
4fea3d778a
backup
2017-06-23 18:57:00 -04:00
Heng Li
mbrcic
Hasindu Gamaarachchi
Hasindu Gamaarachchi