44754cd615
r731: separate layouter
2014-04-28 10:39:29 -04:00
dadd5d6281
r730: more permissive about merging overlapping
2014-04-28 10:01:54 -04:00
76bb49e01b
r729: halved band width; doubled patch band width
2014-04-24 16:06:01 -04:00
6052d3015b
r728: sorting the end in mem_sort_dedup_patch()
...
The older version does this, which is correct.
2014-04-24 15:44:59 -04:00
df65893fb5
r727: extend seeds with SW
2014-04-24 14:28:40 -04:00
b92bbb47e5
Merge branch '0.7.7-softclip' into layout
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Conflicts:
Makefile
bwamem.h
fastmap.c
main.c
2014-04-24 12:24:49 -04:00
8c12ec4a4b
r725: optionally disable hard clipping
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as is reqested by the cancer group
2014-04-24 11:56:43 -04:00
b93fca2b2e
r723: merge adjacent hits
2014-04-16 16:38:50 -04:00
48847af2fc
code backup
2014-04-16 12:00:13 -04:00
00a07f61bf
r721: merge overlapping hits by default
2014-04-15 16:16:04 -04:00
45f24b4ae8
r720: improved overlap hit merging
2014-04-15 16:09:42 -04:00
bdb7b000cd
r719: more stringent overlap merge
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Will consider to make it the default
2014-04-15 14:52:17 -04:00
4e22270eba
r718: merge alnregs overlapping on both query/ref
2014-04-14 17:01:17 -04:00
6d4a6debdc
r716: changed -x pbread
2014-04-14 16:04:29 -04:00
bbcabfe342
r707: change params for pacbio-to-pacbio
2014-04-10 21:53:52 -04:00
658f27eae4
Merge branch 'dev' into layout
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Conflicts:
main.c
2014-04-10 21:48:47 -04:00
6fda93502f
r705: pairing performed on one chr only
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Change of versioning: the revision number is acquired with:
git rev-list --all --count
This counts the total number of commits across all branches.
2014-04-10 21:38:14 -04:00
db4b171fa6
Merge branch 'dev' into layout
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Conflicts:
main.c
2014-04-10 21:09:47 -04:00
07182d9061
dev-475: -F outputs unit score, not raw score
2014-04-10 21:09:06 -04:00
7d25fe2de3
Merge branch 'dev' into layout
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Conflicts:
main.c
2014-04-10 21:07:16 -04:00
e80bccc923
dev-474: fixed a typo
2014-04-10 21:04:02 -04:00
f02cd42679
dev-473: added a few assertions
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to make sure the new change works as is expected
2014-04-10 21:03:13 -04:00
8638cfadc8
dev-472: get rid of bwa_fix_xref()
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This function causes all kinds of problems when the reference genome consists
of many short reads/contigs/chromsomes. Some of the problems are nearly
unfixable at the point where bwa_fix_xref() gets called. This commit attempts
to fix the problem at the root. It disallows chains spanning multiple contigs
and never retrieves sequences bridging two adjacent contigs. Thus all the
chaining, extension, SW and global alignments are confined to on contig only.
This commit brings many changes. I have tested it on a couple examples
including Peter Field's PacBio example. It works well so far.
2014-04-10 20:54:27 -04:00
e2d0c996e9
layout-477: output unit score, not the raw score
2014-04-10 18:03:28 -04:00
0eeacbbe39
Merge branch 'dev' into layout
2014-04-10 17:56:24 -04:00
23e0e99ec0
dev-471: fixed a compiling error from last commit
2014-04-10 11:54:17 -04:00
ccbbe48c4f
dev-470: don't stop on bwa_fix_xref2() failures
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Peter Field has sent me an example caused by an alignment bridging three
adjacent chromosomes/contigs. Bwa-mem always aligns the query to the contig
covering the middle point of the alignment. In this example, it chooses the
middle contig, which should not be aligned. This leads to weird things failing
bwa_fix_xref2(), which cannot be fixed unless we build the contig boundaries
into the FM-index.
In the old code, bwa-mem halts when bwa_fix_xref2() fails. With this commit,
bwa-mem will give a warning instead of halting.
2014-04-10 11:43:17 -04:00
8220008564
an attempt to layout tool
2014-04-09 16:11:52 -04:00
db58392e9b
dev-469: fixed wrong command line prompt
2014-04-09 13:20:04 -04:00
d766591c1e
dev-468: fixed a segfault caused by NULL
2014-04-08 22:11:36 -04:00
99f6f9a0d1
dev-467: limit the max #chains to extend
2014-04-08 21:45:49 -04:00
c0a308a8b6
dev-466: simplified chain filtering
2014-04-08 17:33:07 -04:00
f12dfae772
dev-465: a new output format for read overlap
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Also moved a few functions to bwamem_extra.c. File bwamem.c is becoming far too
long.
2014-04-08 16:29:36 -04:00
b45aeb87e1
dev-464: preset for pacbio read2read aln
2014-04-08 11:40:54 -04:00
172ba83241
dev-463: added option -x to change multiple params
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I hate to copy-paste long command line options.
2014-04-07 11:29:36 -04:00
114901b005
dev-r462: refined setting for PacBio; weight flt
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The recommended setting in the last commit is wrong. If we can extend a random
seed hit to the full length, we will force the read aligned through break
points, which is wrong. The new setting is better but it may lead to a small
fraction of fragmented alignments.
In addition, I added a filter on the minimum chain weight and tied
min_HSP_score to this filter. It doubles the mapping speed.
2014-04-04 17:01:04 -04:00
41f720dfa7
dev-461: added a heuristic for PacBio data
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See the comment above mem_test_chain_sw() for details.
2014-04-04 16:05:41 -04:00
066ec4aa95
dev-460: disallow a cigar 20M2D2I30M in extension
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Global alignment does not allow contiguous insertions and deletions, but local
alignment and extension allow such CIGARs. The optimal global alignment may
have a lower score than extension, which actually happens often for PacBio
data. This commit disallows a CIGAR like 20M2D2I30M to fix this inconsistency.
Local alignment has not been changed.
2014-04-04 10:44:34 -04:00
b6bd33b26c
dev-459: don't hard code the drop ratio
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In the old code, if a secondary alignment is 50% worse, it won't be outputted.
2014-04-03 18:58:49 -04:00
b3225581be
dev-458: simplified the smem iterator
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simpler but less powful.
2014-04-03 15:23:48 -04:00
acfe7613db
dev-457: separated interval collection and seeding
2014-04-03 15:10:50 -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
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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
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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
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
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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
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
Heng Li
Bradford Powell
John Marshall
Rob Davies