9649f3496f
Merge branch 'dev'
2014-12-02 10:35:02 -05:00
393735d7f1
more FAQs on ALT mapping
2014-12-02 10:30:35 -05:00
ae4aa77b50
Merge branch 'dev'
2014-12-01 09:51:05 -05:00
d6e8e5929b
Updated READMEs a little
2014-12-01 09:50:47 -05:00
309d1c543d
Merge branch 'dev'
2014-11-26 13:27:21 -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
cb8992459f
Merge branch 'dev'
2014-11-19 12:54:30 -05:00
3633436a3d
added download link explicitly
2014-11-19 12:54:15 -05:00
decc812f77
Merge branch 'dev'
2014-11-19 12:47:20 -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
8422950472
Merge branch 'dev'
2014-11-19 12:33:18 -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
7e29a01b77
Merge branch 'dev'
2014-11-19 12:30:03 -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
b31992991a
Merge branch 'dev'
2014-11-19 09:37:10 -05:00
bb7a97f68c
update about bwa.kit
2014-11-19 09:36:56 -05:00
82ef0500e6
Merge branch 'dev'
2014-11-18 23:29:11 -05:00
56f1056b49
don't type empty files
...
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
050482ef77
fine tune
2014-11-13 19:52:47 -05:00
65c637b036
smarter prefix finder
2014-11-13 16:16:21 -05:00
4373a077d5
wrapper for bwa-mem
2014-11-13 15:51:00 -05:00
a5c144db4d
added scripts to generate hs38a.fa and hs38d6.fa
2014-11-13 12:53:29 -05:00
fffe52a45b
move bwa-typeHLA back to this repo
2014-11-13 12:50:56 -05:00
904afefbc6
r985: fix bug due to the lack of _pri contigs d6
2014-11-13 12:12:41 -05:00
c5fe18438a
r984: updated to the latest kseq.h
2014-11-13 11:12:23 -05:00
7eabcf42c4
r983: bugfix - wrong mate info
...
Picard now gives a clean bill.
2014-11-10 13:15:11 -05:00
a81603217e
mate chr is sometimes wrong
2014-11-10 10:16:53 -05:00
b2b42cea7e
removed contig weight & code cleanup
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Contig weight was calculated based on a false assumption. It is actually not useful.
2014-11-07 12:45:01 -05:00
4e97cdfde8
move to a new project bwa-typeHLA
...
The two scripts cannot be used standalone anyway.
2014-11-06 09:13:15 -05:00
c2f2cb03ce
to be moved to a separate project
2014-11-06 09:12:53 -05:00
1bee29ef44
map to individual HLA ALT for meaningful mapQ
2014-11-06 00:37:59 -05:00
10de1e0b74
optionally output debegging info
2014-11-05 13:20:33 -05:00
0eee4fa1b0
nothing, really
2014-11-04 16:00:25 -05:00
2a41772d0a
more command line help
2014-11-04 15:41:18 -05:00
e5d7f4fc30
change the default max_len
2014-11-04 15:31:33 -05:00
ccf03ffd22
control min-match-length
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we still need this to kill false mapping/alignment
2014-11-04 15:26:10 -05:00
Heng Li