0168f39eeb
r765: fixed a declaration error
...
Reported by Andreas Tile from Debian
2014-05-13 12:54:23 -04:00
08517ac09b
r764: changed -c in "-x pacbio" to 500
2014-05-13 12:53:24 -04:00
39a6cd5bb0
r762: cleanup for the new release; unfinished
...
It will take to make the documentation ready.
2014-05-11 15:15:44 -04:00
cfe6996173
r760: removed commented code
...
It is slow and is not very effective. And I hate useless code.
2014-05-09 14:59:07 -04:00
43b498a37e
r759: bugfix - frac_rep not working
...
Also added commented code for a 3rd round seeding. Not used.
2014-05-09 14:56:59 -04:00
c9b33502f3
r758: fixed a typo
...
mostly negligible in practice
2014-05-07 15:07:29 -04:00
6ac8dd5840
r754: added command msg for -h
2014-05-06 16:15:14 -04:00
ce3c198245
r749: max_hits tunable on CMD; default to 5
2014-05-04 10:17:03 -04:00
f21d6498bc
r748: reduced the default -m to 50
2014-05-02 16:49:19 -04:00
e8f28cb529
r747: fixed a minor issue in the last (mis)commit
2014-05-02 16:17:50 -04:00
6db761e269
r746: tuned heuristic for GRCh38
...
Reduced -c to 500 by default. As a compensation, we choose up to 1000 positions
if a seed has 500 or more occurrences. In addition, a read with big portion
from such seeds will have lower mapping quality.
2014-05-02 16:06:27 -04:00
b7076848ab
r744: int overflow given MB query
2014-05-01 15:30:36 -04:00
fa20c71920
r742: further control the max bandwidth
...
I am looking at 6kb bandwidth...
2014-05-01 14:27:38 -04:00
7954e77a1b
r741: fixed segfault in rare cases
2014-05-01 11:13:05 -04:00
4b2441069f
r740: don't attempt merge if bandwidth too large
...
Sometimes the bandwidth can be >10k.
2014-05-01 11:01:52 -04:00
5aedc978d1
r739: output suboptimal hits in the PE mode
...
However, PE information is not used for suboptimal hits
2014-04-30 23:23:54 -04:00
c6c943f9d7
r738: output multi-map in the XA tag (SE only)
...
... PE support coming soon
2014-04-30 16:46:05 -04:00
d59d78838c
r737: fixed an assertion when failed to convert sa
...
A bug pointed out by Mikkle Schubert
2014-04-30 14:55:44 -04:00
88f89be60e
r736: improved in low-complexity regions
...
Example: GGAGGGGAAGGGTGGGCTGGAGGGGACGGGTGGGCTGGAGGGGAAGGGTGTGCTGGAGGGAAAAGGTGGACTGGAGGGGAAGGGTGGGCTGGAGGGGAAGG
This read has 5 chains, two of which are:
weight=80 26;26;0,4591439948(10:-3095894) 23;23;27,4591439957(10:-3095888) 31;31;70,4591439964(10:-3095873)
weight=50 45;45;51,4591440017(10:-3095806) 50;50;51,4591440017(10:-3095801) 31;31;70,4591440090(10:-3095747)
Extension from the 26bp seed in the 1st chain gives an alignment [0,101) <=> [4591439948,4591440067), which
contains the 50bp seed in the second chain. However, if we extend the 50bp seed, it yields a better alignment
[0,101) <=> [4591439966,4591440067) with a different starting position. The 26bp seed is wrong. This commit
adds a heuristic to fix this issue.
2014-04-30 14:14:20 -04:00
11698fc4e5
r735: fixed a bug caused by merge
2014-04-30 13:12:43 -04:00
b603fed39c
r733: bugfix - seed score unset when no -W
2014-04-29 14:58:53 -04:00
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
...
Conflicts:
Makefile
bwamem.h
fastmap.c
main.c
2014-04-24 12:24:49 -04:00
8c12ec4a4b
r725: optionally disable hard clipping
...
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
...
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
...
Conflicts:
main.c
2014-04-10 21:48:47 -04:00
6fda93502f
r705: pairing performed on one chr only
...
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
...
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
...
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
...
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()
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
...
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
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
...
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
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
...
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
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
1346f03ff1
use the old mapQ by default
...
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
...
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
...
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
...
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
...
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.
...
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
...
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
...
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
...
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
...
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.
...
Conflicts:
bwt.c
2013-04-11 11:15:39 +01:00
499cf4c00d
r376: reduce wasteful seed extension
...
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
...
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
...
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
...
to avoid misalignment in tandem repeats
2013-04-04 00:43:43 -04:00
1e118e0823
r370: suppress "D" at the end of a cigar
...
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
c89756e2b0
Merge branch 'master' into master_fixes
2013-03-19 12:11:51 +00:00
8437cd4edd
r369: bugfix - segfault caused by the last change
...
Sigh... Even the simplest change can lead to new bugs.
2013-03-19 01:04:57 -04:00
1e3cadbfc2
r368: bugfix - wrong CIGAR when bridging 3 contigs
...
In this case, bwa_fix_xref() will return insane coordinates. The old version
did not check the return status and write wrong CIGAR. This bug only happen to
very short assembly contigs.
2013-03-18 20:49:32 -04:00
c862a1a396
Merge branch 'master' into master_fixes
2013-03-18 13:35:12 +00:00
9346acde1b
Release bwa-0.7.3a-r367
...
In 0.7.3, the wrong CIGAR bug was only fixed in one scenario, but not fixed
in another corner case.
2013-03-15 21:26:37 -04:00
7dec00c217
Release BWA-0.7.3-r366
2013-03-15 12:51:53 -04:00
dd51177837
r365: bugfix - wrong alignment (right mapping)
...
The bug only happens when there is a 1bp del and 1bp ins which are close to the
end and there are no other substitutions or indels. In this case, bwa mem gave
a wrong band width.
2013-03-15 11:59:05 -04:00
e5355fe3a0
r364: bug in mem pairing (no effect with -A=1)
...
Forgot to adjust for matching score. This bug has no effect when -A takes the
default value.
2013-03-14 22:01:26 -04:00
cca27c1ef5
Merge branch 'master' into master_fixes
...
Conflicts:
bwamem.c
bwamem_pair.c
example.c
2013-03-13 12:12:28 +00:00
bdf34f6ce7
r363: XA=>XP; output mapQ in XP
...
In BWA, XA gives hits "shadowed" by the primary hit. In BWA-MEM, we output
primary hits only. Primary hits may have non-zero mapping quality.
2013-03-12 09:56:04 -04:00
c29b176cb6
r362: bugfix - occasionally wrong TLEN
...
Use the 0.7.2 way to compute TLEN
2013-03-12 00:14:36 -04:00
aa7cdf4bb3
r361: flag proper pair even if multi-primary
...
Up to here, all the features in my checklist have been implemented.
2013-03-12 00:00:04 -04:00
dab5b17c1a
r360: output alternative primary alignments in XA
2013-03-11 23:43:58 -04:00
6c665189ad
r359: identical output to 0.7.2 (without -a)
2013-03-11 23:16:18 -04:00
9228e48efd
Merge branch 'master' into master_fixes
...
Conflicts:
Makefile
2013-03-11 13:50:49 +00:00
5581cb9152
Release bwa-0.7.2-r351
...
For the TLEN sign fix. Sorry for the significant bug in 0.7.0/0.7.1
2013-03-09 18:15:41 -05:00
2d01a297fb
Improving 'properly paired' flag.
...
If one end has a low quality tail that happens to have a score-20 hit,
the pair won't be flagged as properly paired because bwa-mem thought it has
multiple hits. By filtering with -T, we won't have this problem.
2013-03-09 18:05:50 -05:00
Heng Li
Bradford Powell
John Marshall
Rob Davies