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
1993cb634d
Split README-alt.md into two documentations
2014-11-19 12:29:35 -05:00
9ade171f7a
transfer read groups from the input BAM
2014-11-19 11:43:59 -05:00
b5f6ed3020
r1005: insert arbitrary header lines
2014-11-19 10:59:05 -05:00
15c93e7a52
renamed extras to bwakit for clarity
2014-11-19 10:37:03 -05:00
bb7a97f68c
update about bwa.kit
2014-11-19 09:36:56 -05:00
56f1056b49
don't type empty files
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This causes errors.
2014-11-18 23:28:46 -05:00
61ab329639
fine tune the wrapper scripts
2014-11-18 15:40:58 -05:00
80e4ecfa79
r998: smart pairing; allow mixture of SE/PE reads
2014-11-18 14:30:22 -05:00
6f9bf9a4ae
minor change
2014-11-17 15:23:38 -05:00
eb664c2fe8
added an evaluation section
2014-11-17 14:54:24 -05:00
cee8149b12
Updated README for ALT mapping
2014-11-17 13:20:23 -05:00
ad9d12c04d
Removed a comment on hs38 lacking EBV
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as is pointed out by Martin Pollard
2014-11-17 11:08:07 -05:00
bf053c779b
polish
2014-11-17 10:54:16 -05:00
0071c4ab22
polish the run script
2014-11-17 10:44:54 -05:00
792be78a80
replace run-gen-hs38* with run-gen-ref
2014-11-16 00:46:02 -05:00
Heng Li
Mike Covington