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
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
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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
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
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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
1346f03ff1
use the old mapQ by default
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the new mapQ overestimate
2013-09-06 14:04:41 -04:00
ed78df9184
Merge branch 'master' into clip2
2013-08-28 16:00:34 -04:00
3b84c03c1e
r406: allow to use diff clipping penalties
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for 5'-end or for 3'-end
2013-08-28 15:59:05 -04:00
b88718d8f4
Reformat note for 80 columns, and fix typo
2013-06-14 14:03:08 +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
73619754f8
r401: bugfix - forgot to change sampe
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some changes to samse should also be applied to sampe
2013-05-27 22:24:35 -04:00
599e840779
r397: multi changes/bugfixes to bwa-backtrack
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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
bde5005f39
r396: er... the new tag is named SA not SP
2013-05-23 12:48:18 -04:00
3d2450ed97
r395: bugfix - hard clipping not applied on revaln
2013-05-23 12:45:14 -04:00
9441bb7f2a
r394: added future plan
2013-05-22 20:02:53 -04:00
9a6abe51b6
r391: better method to resolve xref alignment
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The old method does not work when the alignment bridges three chr. This may
actually happen often. The new method does not work all the time, either, but
should be better than the old one. It is also simpler, arguably.
2013-05-22 18:57:51 -04:00
e88529687f
Merge branch 'master' into master_fixes. Merged up to r389.
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Conflicts:
bwamem.c
kopen.c
2013-04-29 12:09:30 +01:00
1a2bd2cf91
r389: return non-zero upon errors
2013-04-27 10:08:01 -04:00
19cb7cd7ed
r388: cleanup mem_process_seqs() interface
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Print output outside the function and allow to feed insert size distribution.
2013-04-26 12:31:18 -04:00
8896cb942e
r386: bugfix - samse/pe segfault
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This happens when a read is aligned across the forward-reverse boundary.
2013-04-24 16:00:02 -04:00
b3d0a13b32
Merge branch 'master' into master_fixes. Merged up to release bwa-0.7.4-r385.
2013-04-23 17:31:34 +01:00
c14aaad1ce
Released bwa-0.7.4-r385
2013-04-23 11:40:56 -04:00
2f6897c72b
r384: don't compile bwamem-lite by default
2013-04-23 11:27:30 -04:00
78ed00021f
r384: updated NEWS
2013-04-23 11:25:46 -04:00
4cb5110d03
Merge branch 'master' into master_fixes
2013-04-22 09:51:07 +01:00
f6ae0d4d0f
r382: similar treatment in bwa-sw (see r381)
2013-04-19 17:52:06 -04:00
3f8caef33c
r381: fixed a bug when upper bound < max read len
2013-04-19 17:44:35 -04:00
db7a98636f
r380: er... another compiling error
2013-04-19 12:04:44 -04:00
f0c94d80d1
r379: fixed compiling error
2013-04-19 12:04:00 -04:00
be11e27e12
r378: bugfix - wrong CIGAR
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This is actually caused by a bug in SSE2-SW, where the query begin may be
smaller than the true one if there is an exact tandem repeat.
2013-04-19 12:00:37 -04:00
2087dc162f
r377: increased unpaired penalty from 9 to 17
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This leads to more aggressive pairing - more properly paired reads. I have
found a few cases where, for example, read1 is umambiguously mapped to chr20
while its 100bp mate has a perfect match to another chr but has 3 mismatches
and 1 deletion when it is paired with read1 on chr20. With longer reads, it
seems that the chr20 hit is correct, although it is not obvious how this
happened in evolution.
2013-04-17 16:50:20 -04:00
3dd10bd7db
Merge branch 'master' into master_fixes
2013-04-12 16:20:13 +01:00
90ecd344ba
Merge branch 'master' into master_fixes. Merged up to master r375.
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Conflicts:
bwt.c
2013-04-11 11:15:39 +01:00
499cf4c00d
r376: reduce wasteful seed extension
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mainly for contig alignment
2013-04-10 12:18:56 -04:00
47520134e7
r375: fixed compiling errors by the last change
2013-04-10 11:04:32 -04:00
3d8a8c1e37
r374: fix - clipping penalty not always working
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This only happens to gaps where mem underestimates the bandwidth without
considering the clipping penalty.
2013-04-10 01:09:37 -04:00
53bb846407
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
d64eaa851d
fixed an issue caused by a Mac/Darwin bug
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On Mac/Darwin, it is not possible to read >2GB data with one fread().
2013-04-09 15:17:04 -04:00
d7ca0885eb
r371: extend overlapping seeds
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to avoid misalignment in tandem repeats
2013-04-04 00:43:43 -04:00
1e118e0823
r370: suppress "D" at the end of a cigar
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This is caused by seeds in tandem repeats, in which case, bwa-mem may not
extend the true seed. The change in this commit is only a temporary cure.
2013-04-03 23:57:19 -04:00
Bradford Powell
Heng Li
John Marshall
Rob Davies