c982443210
r854: improved the calculation of pa
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and build pa filtering into BWA-MEM
2014-09-17 16:26:28 -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
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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
5d26ab0ee3
r828: changed the default scoring for pacbio
2014-09-15 23:22:05 -04:00
35ac99b4f7
r815: optionally output ref fasta header
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Also fixed a bug in reading .ann files
2014-08-29 10:51:23 -04:00
b5cba257c1
r809: new strategy for the -a mode
2014-08-25 11:59:27 -04:00
08517ac09b
r764: changed -c in "-x pacbio" to 500
2014-05-13 12:53:24 -04:00
a35a6c2580
updated maual page
2014-05-12 12:52:16 -04:00
39a6cd5bb0
r762: cleanup for the new release; unfinished
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It will take to make the documentation ready.
2014-05-11 15:15:44 -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
11698fc4e5
r735: fixed a bug caused by merge
2014-04-30 13:12:43 -04:00
76bb49e01b
r729: halved band width; doubled patch band width
2014-04-24 16:06:01 -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
00a07f61bf
r721: merge overlapping hits by default
2014-04-15 16:16:04 -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
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
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
...
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
b3225581be
dev-458: simplified the smem iterator
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simpler but less powful.
2014-04-03 15:23:48 -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
...
This is also very useful for debugging.
2014-03-31 11:21:03 -04:00
9ce50a4e5e
dev-450: support diff ins/del penalties. NO TEST!!
2014-03-28 14:54:06 -04:00
2e9463ebf1
dev-r442: suppress exact full-length matches
2014-02-26 22:04:19 -05:00
ce026a07fc
r439: expose mem_opt_t::max_matesw
2014-02-19 13:10:33 -05:00
10cb6b0507
r428: allow to change the default chain_drop_ratio
2013-12-30 16:18:45 -05:00
4219e58623
r423: bugfix - SE hits not random
2013-11-23 09:36:26 -05:00
c564653b40
r416: removed a line of debugging code
2013-09-12 10:41:43 -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
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
128ffc089b
Complain when bwa mem is given too many filenames
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Reads in extra .fq filenames beyond "bwa mem index one.fq two.fq"
will not be aligned, so complain about such invalid usage instead.
2013-06-14 14:00:24 +01:00
9735d7a31a
conform to the latest (unpublished) SAM spec
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for chimeric alignments
2013-05-22 19:45:16 -04:00
0aa7e0a402
Ensure exit status of 1 if given invalid options or index files are not found.
...
Added missing default cases in option scanning.
Ensure exit value is 1 if bwa_idx_load or bwa_idx_infer_prefix fail.
These changes extend the previous one, which only fixed the mem aligner.
2013-04-29 13:58:28 +01:00
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
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
53bb846407
r373: optionally distable mate rescue
2013-04-09 16:13:55 -04:00
aabd990e8f
Merge branch 'master' into master_fixes
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Conflicts:
Makefile
bwape.c
bwase.c
bwtsw2_aux.c
stdaln.c
2013-03-08 16:46:45 +00:00
b0a76884e8
r340: feature freeze; updated the manpage
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I will stop adding new features to bwa and prepare for the next release. I will
briefly evaluate the variant calling accuracy before the release.
2013-03-07 11:51:23 -05:00
3e3236dfc4
r337: mem - always read even number of reads
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In the old code, we may read odd number of reads from an interleaved fastq.
2013-03-07 11:00:15 -05:00
5fbd454682
r332: added output threshold
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Otherwise there are far too many short hits
2013-03-05 22:49:38 -05:00
07921659cf
move mem_fill_scmat() to bwa.{h,c}
2013-03-05 09:38:12 -05:00
8a078cc16d
Merge branch 'master' into master_fixes
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Conflicts:
bntseq.c
bwamem.c
2013-03-05 10:21:07 +00:00
efd9769b07
r324: a little code cleanup
...
The changes after r317 aim to improve the performance and accuracy for very
long query alignment. The short-read alignment should not be affected. The
changes include:
1) Z-dropoff. This is a variant of blast's X-dropoff. I orginally thought this
heuristic only improves speed, but now I realize it also reduces poor
alignment with long good flanking alignments. The difference from blast's
X-dropoff is that Z-dropoff allows big gaps, but X-dropoff does not.
2) Band width doubling. When band width is too small, we will get a poor
alignment in the middle. Sometimes such alignments cannot be fully excluded
with Z-dropoff. Band width doubling is an alternative heuristic. It is based
on the observation that the existing of close-to-boundary high score
possibly implies inadequate band width. When we see such a signal, we double
the band width.
2013-03-05 00:57:16 -05:00
e0991d6a45
r323: added Z-dropoff, a variant of blast's X-drop
2013-03-05 00:34:33 -05:00
6beab5f765
Merge branch 'master' into master_fixes
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Merge changes to commit c5434ac
2013-03-01 10:22:49 +00:00
3d33ab063e
Merge branch 'master' into master_fixes
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Merged to master version b621d3a
2013-03-01 09:37:46 +00:00
4bb0bdddca
r306: introduce clipping penalty
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More clipping leads to more severe reference bias. We should not clip the
alignment unless necessary.
2013-02-27 21:13:39 -05:00
e620f0ff4e
r302: updated the manpage
2013-02-27 13:16:22 -05:00
98787f0ae0
r295: generate NM
2013-02-26 13:36:01 -05:00
9957e04590
r278: don't perform too many mate-sw
2013-02-25 11:56:02 -05:00
5092211d75
controllable scoring matrix
2013-02-25 11:24:21 -05:00
5ead86acd3
optionally mark split hit as secondary
2013-02-25 11:18:35 -05:00
4dc982a3c7
support interleaved fastq
2013-02-25 00:13:32 -05:00
0b4a40dc25
updated revision number; to merge into master
2013-02-24 13:34:20 -05:00
85775c3384
output multiple hits
2013-02-24 13:23:43 -05:00
6bdccf2a8a
added a bit documentation
2013-02-24 13:09:29 -05:00
6e7903e9f3
added kopen support
2013-02-23 17:09:23 -05:00
b4c38bcc1c
append fasta/q comment
2013-02-23 16:57:34 -05:00
ee4540c394
support read group in bwa-mem
2013-02-23 16:41:44 -05:00
67543f19a1
code refactoring
2013-02-23 15:55:55 -05:00
3c330d5049
for another round of code cleanup
2013-02-23 15:12:26 -05:00
d460f2ec9e
bugfix in multi-threaded bwa-mem
2013-02-23 14:48:54 -05:00
f122fad562
minor code clean up
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bwtio.c is merged to bwt.c
2013-02-22 17:09:40 -05:00
54da54ffd4
extend more seeds (and thus slower...)
2013-02-21 12:52:00 -05:00
66585b7982
code backup
2013-02-18 16:33:06 -05:00
95d18449b3
merge bseq.{h,c} to utils.{h,c}
...
I do not like many small files.
2013-02-12 10:36:15 -05:00
987d4b4205
fixed a stupid bug in fastq reading
2013-02-11 11:27:35 -05:00
59eaf650ac
code backup
2013-02-11 10:59:38 -05:00
cb55617f50
added a new line
2013-02-08 22:12:18 -05:00
95a79afe71
command-line prompt
2013-02-08 22:11:44 -05:00
39607065e0
allow more seeds to be seen (thus slower..)
2013-02-08 16:56:28 -05:00
cd6bd524d4
discard internal seeds shorter than half
2013-02-07 19:50:37 -05:00
ff3fea115c
write soft clip; added debugging code
2013-02-07 16:27:11 -05:00
1fd51fc3f7
code backup
2013-02-07 14:36:18 -05:00
5dc398cdef
start to write CLI
2013-02-07 13:13:43 -05:00
5a0b32bfd2
updated to the latest kseq.h
2013-02-06 14:38:40 -05:00
a9292d674d
a bit code cleanup
2013-02-06 13:59:32 -05:00
a61288c768
separate CIGAR generation
2013-02-05 21:49:19 -05:00
1e16f3e701
calling ksw_global(); ksw_extend() is buggy!
2013-02-05 17:13:12 -05:00
d6a73c9171
chain filtering apparently working
2013-02-05 00:17:20 -05:00
9d0cdb2d3c
unfinished chain filter
2013-02-04 17:23:06 -05:00
788e9d1e3d
fixed a couple of leaks; buggy atm
2013-02-04 15:40:26 -05:00
ba18db1a9f
sw extension works for the simplest case
2013-02-04 12:37:38 -05:00
d25a87cc50
code backup
2013-02-02 15:14:24 -05:00
00e5302219
routine to get subsequence from 2-bit pac
2013-02-01 16:39:50 -05:00
f8f3b7577a
code cleanup; added a missing file
2013-02-01 14:38:44 -05:00
Heng Li
John Marshall
Rob Davies