beff2e27f8
Add missing <stdint.h> include
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Fixes compilation on non-glibc platforms, e.g., FreeBSD and Alpine Linux.
2017-04-25 13:54:31 +01:00
af87825525
Replace u_int32_t by the more common uint32_t
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The u_int32_t type comes from <sys/types.h>, which is often included
as a byproduct of other headers on glibc platforms, but not on FreeBSD
or Alpine Linux. Use <stdint.h>'s uint32_t instead, which is used
elsewhere in bwa source code.
2017-04-25 13:51:52 +01:00
f123871451
r1142: added option -5 for Hi-C data
2016-05-31 11:01:36 -04:00
850dd811fc
Release bwa-0.7.15-r1140
2016-05-31 09:42:50 -04:00
58bcc251f2
r1138: fixed typo in insert size estimate ( #65 )
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credit to @sjackman
2016-05-20 18:05:15 -04:00
5db0c362f5
Release 0.7.14-r1136
2016-05-04 14:41:37 -04:00
7ec3261877
r1134: use AH:* instead of AH:Y
2016-05-03 11:28:58 -04:00
3c038250f9
r1130: changed "ah" to "AH"
2016-04-28 15:39:18 -04:00
9e5852c540
Released bwa-0.7.13 (r1126)
2016-02-23 11:24:19 -05:00
b94a78adbf
use /usr/env/perl
2016-02-23 11:08:43 -05:00
f1ce529cd9
added comment
2016-02-23 11:08:11 -05:00
11437a14f4
Port #48 to the dev branch
2016-02-23 11:07:27 -05:00
9a828344ec
moved indexing to libbwa
2016-02-13 18:48:46 -05:00
86170ffd2f
r1102: resumed versioning
2016-02-01 11:57:14 -05:00
ede7b092a2
updated GRCh38 download link
2016-02-01 11:50:25 -05:00
1e6a10ce2d
a typo in fastmap command-line prompt
2016-02-01 11:41:46 -05:00
6f0ea0b7e3
use /usr/bin/env perl
2016-02-01 11:39:50 -05:00
fdf47000e7
integer overflow on indexing
2016-01-26 23:21:23 -05:00
c819643412
make kthread.c compiled with g++
2016-01-26 22:49:28 -05:00
1247dc2346
removed the pbread mode
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It is not working well. Not at all.
2016-01-26 22:37:01 -05:00
616a53491d
Merge branch 'dev' of github.com:lh3/bwa into dev
2016-01-26 17:19:16 -05:00
feeb41f42d
updated dependencies
2016-01-26 13:54:47 -05:00
be2020c4af
ropebwt2 for bwt construction
2016-01-26 13:46:08 -05:00
e3ea2a8222
Merge pull request #47 from mfcovington/feature/fix-maxk-error
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Include 'unistd.h' to explicitly declare 'getopt'
2015-11-14 20:47:22 -05:00
c2efebefa7
Include 'unistd.h' to explicitly declare 'getopt'
2015-11-14 17:27:57 -08:00
6c668d3e1a
fixed a bug in reverse-complement
2015-08-27 10:44:08 -04:00
3ae437ac13
r1044: fixed an out-of-order bug in kthread
2015-03-25 12:16:06 -04:00
163f949a33
added maxk: max unique k-mer at each position
2015-02-08 16:49:25 -05:00
1f99921b73
changed download link: 0.7.11 => 0.7.12
2014-12-29 16:43:22 -05:00
8211fbcb62
Released 0.7.12
2014-12-28 15:44:59 -05:00
e746a3eac7
r1038: wrong 0x100|0x800 flags in PE mode
2014-12-24 13:22:46 -05:00
3ae8d4b80b
r1037: wrong read number flag
2014-12-24 00:55:33 -05:00
b9bbf2d3df
r1036: PE ALT mapping incorrect
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No SA/XA tags!
2014-12-24 00:49:50 -05:00
408fd5e072
Released bwa-0.7.11-r1034
2014-12-23 15:29:18 -05:00
d7ce7e1395
hs38D1=>hs38DH; cmd help for run-gen-ref
2014-12-23 11:48:59 -05:00
ed95769a33
updated documentations
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(prepare for release)
2014-12-21 16:30:29 -05:00
c05a721f28
improved doc and don't type HLA by default
2014-12-21 00:12:11 -05:00
5aba188969
write empty .gt file as a placeholder
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to suppress error messages from run-bwamem
2014-12-20 22:27:27 -05:00
32c4e3fe5a
updated decoy sequences and names
2014-12-20 22:24:13 -05:00
c561759222
r1027: segfault caused by the last commit
2014-12-12 16:56:54 -05:00
925ddfb697
r1025: accept file with -H; allow to replace @SQ
2014-12-11 10:38:36 -05:00
efa0dd561a
wrong sentence in README-alt
2014-12-10 23:20:46 -05:00
393735d7f1
more FAQs on ALT mapping
2014-12-02 10:30:35 -05:00
d6e8e5929b
Updated READMEs a little
2014-12-01 09:50:47 -05:00
9d8c906e4c
r1017: process I/O in a separate thread
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Previously, bwa-mem waits for I/O. When the input data comes from a slow source
(I/O or piped from a slow program), bwa-mem may spend significant amount of
wall-clock time in the single-thread mode. The same may also happen when bwa-mem
writes to slow target. This commit uses two sequence buffers. it allows bwa-mem
to map one buffer while filling or dumping the other buffer. When bwa-mem is run
on 16 threads using the bwa.kit pipeline, the wall clock time is reduced by 30%.
2014-11-26 12:32:48 -05:00
3633436a3d
added download link explicitly
2014-11-19 12:54:15 -05:00
6609bafa17
moved directory structure to this README
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There are too many README files...
2014-11-19 12:45:21 -05:00
d58beeee56
smarter about path finding
2014-11-19 12:38:55 -05:00
d36083bdc5
minor changes
2014-11-19 12:33:06 -05:00
84024101fa
minor fix to a link
2014-11-19 12:31:32 -05:00
John Marshall
Heng Li
Mike Covington