c280274331
r911: check before attempting adding
2014-10-17 12:13:09 -04:00
76a365a95f
r907: revert to -g.8 by default
2014-10-16 15:56:33 -04:00
d8d8b230d1
r906: don't reduce non-ALT mapQ by default
2014-10-16 15:15:23 -04:00
e318d8e7e5
r905: lower peak RAM for "shm -f"
2014-10-16 11:22:09 -04:00
ad0da1418f
r904: optionally create tmp files for shm staging
2014-10-16 10:52:59 -04:00
97a3102c89
r903: updated revision number
2014-10-16 10:26:25 -04:00
6a0952948d
shared memory
2014-10-15 14:44:08 -04:00
c5e859b49f
r898: read the index into a single memory block
...
Prepare for shared memory. Not used now.
2014-10-15 12:27:45 -04:00
71277f0fea
r896: more flexible ALT reading
2014-10-14 23:37:24 -04:00
2a18fa114f
r895: increase the default max_XA_hits_alt to 200
...
Because there are >100 HLA haplotypes
2014-10-14 16:58:42 -04:00
df20911110
r890: bns_intv2rid() may wrongly return -1
2014-10-14 14:49:53 -04:00
7b62fbb4ba
r880: bug in writing .ann file
2014-10-02 15:34:49 -04:00
a03d01f944
r878: XA is given to the best alignment
...
Non-ALT hits may get ALT hits in the XA tag. This will simplify haplotype
assignment.
2014-09-30 13:50:51 -04:00
0a2cf98293
r876: optionally ignore idxbase.alt file
2014-09-27 23:21:50 -04:00
dae4ca3ced
r875: invalid SAM output for ALT hits
2014-09-26 15:29:08 -04:00
7426a750ec
r868: use soft clip for ALT hits
2014-09-19 16:58:18 -04:00
9af36064e8
r867: fixed a few bugs; added ALT hits to XA
2014-09-19 16:50:21 -04:00
a41afe4c97
These files were committed on a wrong branch
2014-09-18 10:49:35 -04:00
a32d44d8d6
r855: show ALT hits in the PE mode, too
...
In the previous version, it does not
2014-09-17 23:07:56 -04:00
c982443210
r854: improved the calculation of pa
...
and build pa filtering into BWA-MEM
2014-09-17 16:26:28 -04:00
825ae92e58
r849: the pa tag now gives a number
...
... which is the ratio of this hit to the best ALT hit.
2014-09-17 13:05:35 -04:00
6f37c14f26
r848: tag alignments with primary ALT
2014-09-16 18:52:49 -04:00
a458442b24
r845: updated NEWS
...
I will use the new version for a while and then release it.
2014-09-16 14:38:41 -04:00
92bc6849a3
r844: added intra-species contig mapping mode
2014-09-16 10:53:07 -04:00
90518f11e3
r843: presetting for ONT 2d reads
...
Somewhat working for 1d reads, but not very well
2014-09-16 10:38:15 -04:00
4b6eeb34c8
r830: optionally fixed chunk size
2014-09-15 23:42:24 -04:00
624687b072
r829: killed a harmless gcc warning
2014-09-15 23:33:22 -04:00
5d26ab0ee3
r828: changed the default scoring for pacbio
2014-09-15 23:22:05 -04:00
b07587f806
r827: an alt hit as good as a pri hit as supp
2014-09-15 16:07:51 -04:00
bd85af08ab
r826: improved alt mapping for PE
2014-09-15 12:13:04 -04:00
aee53f1334
r824: ALT mapping seems working
2014-09-15 00:29:05 -04:00
015ab3f6c3
r823: towards ALT support
2014-09-14 16:41:14 -04:00
8d2b93156b
r821: more relax on containing seeds
2014-09-12 10:35:49 -04:00
f4aedddee6
r819: bugfix - added too many sub-SMEMs
2014-09-08 11:32:48 -04:00
35ac99b4f7
r815: optionally output ref fasta header
...
Also fixed a bug in reading .ann files
2014-08-29 10:51:23 -04:00
1e611b235c
r810: add err_puts()
...
puts() adds '\n', but fputs() does not.
2014-08-26 11:07:24 -04:00
b5cba257c1
r809: new strategy for the -a mode
2014-08-25 11:59:27 -04:00
bf7d1d46ca
r808: a minor bug with the new index -b
2014-08-25 10:36:24 -04:00
1bba5ef20e
r807: allow to change block size in bwt_gen
...
For a very large reference genome, the default is too small.
2014-08-25 10:31:54 -04:00
705aa53894
Released 0.7.10
2014-07-13 22:57:27 -04:00
7fd6a11569
r788: segfault when the last ref is "weird"
...
mem_patch_reg() did not check if two hits are on the same strand, which may
lead to an alignment bridging the forward-backward boundary.
2014-07-10 10:53:56 -04:00
cffff4338f
r787: use mem_seed_sw() also for non-PacBio reads
...
In the previous version, mem_seed_sw() is only used for PacBio reads to filter
bad seeds. For non-PacBio long queries, bwa-mem uses mem_chain2aln_short() for
a similar purpose. However, it turns out that mem_chain2aln_short() is not
effective given long near-tandem repeats. Bwa-mem still wastes a lot of time
of futile ref substring and extensions.
In this commit, mem_chain2aln_short() has been removed. mem_seed_sw() is used
if the query sequence is long enough (~700bp). For shorter reads, the results
should be almost identical to the previous version.
2014-07-10 10:30:22 -04:00
3efc33160c
0.7.9a-r786: fixed a segfault in a rare case
...
More likely to happen given a circular genome
2014-05-19 16:47:25 -04:00
031d3d83ce
Wrong release number: 0.7.8 => 0.7.9
2014-05-19 09:49:26 -04:00
be74dbc00c
Release bwa-0.7.9-r783
2014-05-19 09:09:11 -04:00
e4752b321b
Release bwa-0.7.9-r782
2014-05-19 09:08:07 -04:00
f00cc94e1d
r779: fixed a memory leak in SE
2014-05-16 00:06:34 -04:00
a5ad0cff7f
r778: reduced the number of alloc() calls a bit
2014-05-15 23:23:04 -04:00
8d2986ece2
r770: fixed a compiling warning
2014-05-14 14:44:03 -04:00
061c63f36a
r766: removed useless code
2014-05-13 13:09:29 -04:00
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
Heng Li