8ede4ffbfa
Fixed clang compiling warnings
2014-03-16 15:18:22 -04:00
1c19bc630f
Released bwa-0.7.7-r441
2014-02-25 01:05:37 -05:00
e879817373
r440: a condition not work due to a typo
2014-02-20 13:06:40 -05:00
ce026a07fc
r439: expose mem_opt_t::max_matesw
2014-02-19 13:10:33 -05:00
17fb85a227
r438: still an issue in MD
...
It occurs when the global alignment disagrees with the local alignment.
2014-02-19 11:31:54 -05:00
52391a9855
r437: print timing for each batch of reads
2014-02-19 10:54:26 -05:00
bdd14d2946
r436: fix rare MD/NM-CIGAR inconsistencies
2014-02-19 10:08:43 -05:00
4adc34eccb
r435: bugfix - base not complemented on the rev
2014-02-18 10:32:24 -05:00
14aa43cca0
r434: added the missing bwasw/aln commands!
2014-02-12 15:39:02 -05:00
7c50bad567
Release bwa-0.7.6a-r433
2014-01-31 12:58:21 -05:00
5fdab3ae13
Released bwa-0.7.6-r432
2014-01-31 11:12:59 -05:00
f524c7d3d8
r431: added the MD tag to bwa-mem
2014-01-29 12:05:11 -05:00
ea3dc2f003
r430: fix a bug producing incorrect alignment
...
Ksw uses two rounds of SSE2-SW to find the boundaries of an alignment. If the
second round gives a different score from the first round, it will fail. The
fix checks if this happens, though I have not dig into an example to understand
why this may happen in the first place.
2014-01-29 10:51:02 -05:00
d17ae1e808
Merge pull request #21 from bpow/fix-duplicate-pg
...
fix duplicate PG lines in bwape and bwase
2014-01-06 06:41:16 -08:00
c26ba4e376
fix duplicate PG lines in bwape and bwase
2014-01-05 14:54:48 -05:00
10cb6b0507
r428: allow to change the default chain_drop_ratio
2013-12-30 16:18:45 -05:00
3afcdc7746
debugging code only: print seeds
2013-12-30 16:05:43 -05:00
74a1a53499
print debugging msg to stdout
2013-12-30 15:49:41 -05:00
f70d80a5a2
r427: fixed bugs in backtrack
...
See comments in ksw_global() for details.
2013-12-30 15:40:18 -05:00
8b6ec74907
r424: fixed a bw bug in samse/pe
2013-11-25 15:48:04 -05:00
4219e58623
r423: bugfix - SE hits not random
2013-11-23 09:36:26 -05:00
29aa855432
r422: matesw hits not sorted
2013-11-21 14:43:50 -05:00
ff4762f3c7
r421: bw doubling in the final alignment
...
In some cases, the band width used in the final alignment needs to be larger
than the band width in extension.
2013-11-20 10:04:16 -05:00
6e3fa0515a
r420: inferred bandwidth is not used in the final
2013-11-20 09:50:46 -05:00
ff6faf811a
r419: print the @PG line
2013-11-19 11:08:45 -05:00
deb19593aa
r418: use the new mapQ estimator by default
2013-11-02 12:25:53 -04:00
19d33faa30
use kthread for multi-threading
...
Bwa-mem should have better performance with many CPU cores.
2013-11-02 12:13:11 -04:00
c564653b40
r416: removed a line of debugging code
2013-09-12 10:41:43 -04:00
7144a0cefc
r415: bug in the new (optional) mapQ computation
...
I may use the new method as the default. Testing needed.
2013-09-09 17:51:05 -04:00
ebb7b02e9b
r414: fixed a bug caused by the last commit
2013-09-09 16:57:55 -04:00
b51a66e4c1
r413: fixed an issue causing redundant alignment
...
I have seen a fosmid aligned to the same position but with two slightly
different CIGARs: 30000M and 29900M50D100M, possibly caused by tandem repeats.
0.7.5a will regard them as two distinct alignments and generates a very small
mapping quality. However, these two are essentially the same. Although there is
ambiguity in aligning the end of the fosmid, we should not penalize the entire
alignment with a small mapQ. This commit fixes this issue. More testing is
needed, though.
2013-09-09 11:36:50 -04:00
1e2cff20ba
more conservative mapQ
2013-09-09 08:57:45 -04:00
1346f03ff1
use the old mapQ by default
...
the new mapQ overestimate
2013-09-06 14:04:41 -04:00
451d60f3be
slight modification
2013-09-06 12:37:38 -04:00
623da055e1
alternative way to estimate mapQ
...
the old mapQ estimate is too conservative
2013-09-06 12:31:47 -04:00
ed78df9184
Merge branch 'master' into clip2
2013-08-28 16:00:34 -04:00
3b84c03c1e
r406: allow to use diff clipping penalties
...
for 5'-end or for 3'-end
2013-08-28 15:59:05 -04:00
426e54740c
Merge pull request #19 from jmarshall/check-qnames
...
Check that input files are name-sorted and the names of paired reads match
2013-06-14 06:27:41 -07:00
b88718d8f4
Reformat note for 80 columns, and fix typo
2013-06-14 14:03:08 +01:00
128ffc089b
Complain when bwa mem is given too many filenames
...
Reads in extra .fq filenames beyond "bwa mem index one.fq two.fq"
will not be aligned, so complain about such invalid usage instead.
2013-06-14 14:00:24 +01:00
20dc9dd41a
Check that paired reads have the same QNAME
...
This detects desynchronised input files, which occasionally happens
due to user error or system failure.
Checking the names just after printing them has no real performance
implications because the strings are already in cache. (It might
be better to check while reading the input, but that would be more
complicated in the two-input-files case.)
2013-06-14 13:57:22 +01:00
7ec8b5c9e7
Release bwa-0.7.5a
2013-05-30 16:20:16 -04:00
ef18cb91cb
Release bwa-0.7.5-r404
2013-05-29 11:49:08 -04:00
01c9cd152b
fixed a typo in NEWS
2013-05-28 13:40:31 -04:00
4e992769d5
r402: updated NEWS (prepare for the 0.7.5 release)
2013-05-28 11:18:42 -04:00
73619754f8
r401: bugfix - forgot to change sampe
...
some changes to samse should also be applied to sampe
2013-05-27 22:24:35 -04:00
6fed8fa0b4
minor changes
2013-05-24 21:17:49 -04:00
02d9bf123f
Minor formatting issues
2013-05-24 20:51:24 -04:00
607e11d43d
updated README
2013-05-24 20:49:36 -04:00
599e840779
r397: multi changes/bugfixes to bwa-backtrack
...
1. Check .sai versioning
2. Keep track of #ins and #del during backtrack
3. Use info above to get accurate aligned regions; don't call SW extension any more
4. Identify alignment crossing the for-rev boundary
5. Fixed a bug in printing the XA tag: ungapped alignments missing
2013-05-24 16:28:18 -04:00
Heng Li
Bradford Powell
John Marshall