1972a97813
Only realloc(pac,...) if it needs to be made larger
...
Similarly to the realloc(pac,...) within add1(), only bother to call
realloc() if appending the reverse complemented sequence requires more
space than is currently in the pac/m_pac buffer.
Avoids realloc(pac,0) (and a "Failed to allocate 0 bytes at bntseq.c"
message from wrap_realloc()) in the corner case of an empty reference
FASTA file. Fixes #54 .
2017-05-10 19:47:12 +01:00
beff2e27f8
Add missing <stdint.h> include
...
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
...
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 )
...
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
...
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
...
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
...
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
...
(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
...
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
...
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
...
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
John Marshall
Heng Li
Mike Covington