9a5705289c
added more debugging infomation
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I can see a bug, but I do not know where it comes from.
2014-04-03 13:38:08 -04:00
3efb7c0e91
r455: release bwa-0.7.8
2014-03-31 15:27:23 -04:00
127c00cc96
dev-454: wording change in command line prompt
2014-03-31 12:03:27 -04:00
b27bdf1ae0
dev-453: change of -A scales -TdBOELU
...
These paramemters are all proportional to -A.
2014-03-31 11:52:52 -04:00
b7076d9023
dev-r452: allow to specify insert size at cmd
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This is also very useful for debugging.
2014-03-31 11:21:03 -04:00
417c6d66c7
dev-r451: fixed a few bugs when -A!=1
...
Something is still wrong.
2014-03-31 10:52:45 -04:00
9ce50a4e5e
dev-450: support diff ins/del penalties. NO TEST!!
2014-03-28 14:54:06 -04:00
578bb55c38
dev-449: unequal ins/del in global() and extend()
2014-03-28 14:15:38 -04:00
0c783399e8
dev-448: different ins/del penalties
2014-03-28 10:54:23 -04:00
8f9aeef4ec
Merge branch 'master' into dev
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Conflicts:
main.c
2014-03-17 00:03:52 -04:00
e6931bec03
r445: unnecessarily large bandwidth in global
2014-03-17 00:01:00 -04:00
7d63e76245
r444: more debugging output in CIGAR generation
...
Also found a potential issue which should not affect accuracy but may hurt
speed. Will investigate later.
2014-03-16 23:25:04 -04:00
8929bd1c25
r443: more verbose debugging information
2014-03-16 15:18:58 -04:00
8ede4ffbfa
Fixed clang compiling warnings
2014-03-16 15:18:22 -04:00
2e9463ebf1
dev-r442: suppress exact full-length matches
2014-02-26 22:04:19 -05:00
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
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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
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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
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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
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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
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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
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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
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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
Heng Li
Bradford Powell