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
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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
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
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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.
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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
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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
Heng Li
John Marshall
Rob Davies