817cb81cb0
Updated README for the HiFi preset
2021-05-01 15:47:25 -04:00
0f5608c4a4
r1028: backport minigraph -U
2021-05-01 15:41:39 -04:00
e8823a3709
r1027: renamed hifi to map-hifi; changed default
2021-05-01 15:22:51 -04:00
7edeec67b0
r1026: fixed bugs in seed sampling add hifi
2021-05-01 15:07:56 -04:00
feb92d32ea
r1025: seed rescuring
2021-04-30 17:33:16 -04:00
cdbd96be0c
a bit refactoring for future changes
2021-04-30 11:24:53 -04:00
ba52c79024
added code of conduct
2021-04-22 17:30:30 -04:00
cd9ccfa069
r1022: check INDEL lengths in simple cases
2021-04-11 22:07:00 -04:00
86b716448c
larger window size for longer INDELs
2021-04-11 16:08:29 -04:00
9ab95be1bb
update END when it is not there
2021-04-11 12:59:21 -04:00
b51e859945
make sure ins/del match
2021-04-11 11:47:14 -04:00
a9037dc16c
r1018: scripts for SV evaluation
2021-04-11 01:08:17 -04:00
9729fa99ad
removed mappy.c
2021-04-09 13:48:16 -04:00
b6ff332de1
Release minimap2-2.18 (r1015)
2021-04-09 13:33:34 -04:00
77abafaaf3
prepare for release
2021-04-09 13:18:56 -04:00
507d39af15
r1013: changed to a more accurate similarity est
...
Based on DOI:10.1101/2021.01.15.426881. One minimap2 reviewer suggested the
right formula to me but I thought the difference would be insignificant. I was
wrong.
2021-04-08 13:57:53 -04:00
827ca4b461
r1012: fixed an off-by-one bug; resolves #489
2021-04-07 23:31:31 -04:00
d3dde2fdd4
Convert from spaces to tabs.
2021-04-05 11:55:10 -04:00
7db2e8d21a
Convert python install from build_ext to setuptools setup_requires.
2021-04-05 11:55:10 -04:00
0b41dd26a2
r1009: fixed a compiler warning
2021-04-05 11:43:13 -04:00
2b47846cd6
r1008: don't parse space in BED
2021-04-05 11:41:00 -04:00
67dd906a80
bump travis python version to 3.9
2021-03-23 09:12:49 -04:00
1b0bb7b0ba
require overlap ratio when considering centromere
2021-03-11 19:11:44 -05:00
1c4b7e8a48
explained --junc-bed in README
2021-03-06 19:44:24 -05:00
ecbc399fa2
improved sveval
2021-03-06 19:44:13 -05:00
4dfd495cc2
added sveval
2021-02-15 14:49:36 -05:00
194b457e79
option to print errors only
2021-02-07 12:58:03 -05:00
75c8933511
evaluate large-scale misjoins
2021-02-07 12:34:13 -05:00
1025993469
print number of errors on each read
2021-01-29 14:08:21 -05:00
a3253d1a6b
added a command for simple VCF statistics
2021-01-14 12:24:38 -05:00
2da649d1d7
Merge remote-tracking branch 'origin/master'
2020-11-15 18:47:15 -05:00
f995f55610
added --mask-len for #659
2020-08-21 11:12:50 -04:00
c9874e2dc5
Initialize r->p if ez->zdropped
2020-06-12 09:22:18 -04:00
28a37a017a
added utg error correction
2020-05-01 00:45:05 -04:00
ccb0f7b05d
added a new Makefile for simde
2020-04-25 22:43:29 -04:00
66db9da7d8
changed preprocessor conditionals for SIMDe
2020-04-22 19:50:59 +02:00
cd2b19035b
r987: position on for strand wrongly outputted
2020-04-22 10:31:25 -04:00
9c0e2c67f8
r986: don't estimate dv with --qstrand
2020-04-21 13:21:03 -04:00
da7109fd29
r985: optionally report cs/cg on the query strand
...
PAF only; not well tested
2020-04-21 12:37:35 -04:00
2b3403f094
fix for Neon after test.
2020-04-21 02:08:21 +02:00
3e16e4e39d
Added documentation entry for added functionality, simde and no_simd.
2020-04-21 01:36:19 +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
29f67a1666
r982: more accurate sum; output errors
2020-04-14 16:18:53 -04:00
adde608a42
Merge remote-tracking branch 'refs/remotes/origin/master'
2020-04-14 15:52:57 -04:00
f10dff78dc
r981: asmgene to check duplicate genes
2020-04-14 15:52:36 -04:00
d97bba9f27
travis: added arm64 test.
2020-04-13 08:33:03 -04:00
50775362bb
r980: support auNGA
2020-04-10 21:36:59 -04:00
0a5e386359
r979: fixed asmgene wrong report. Resolves #581 .
2020-04-06 19:57:15 -04:00
Heng Li
Marcus Stoiber
Armin Töpfer
mbrcic
Jun Aruga