35ac99b4f7
r815: optionally output ref fasta header
...
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
...
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
...
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
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
...
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
b3225581be
dev-458: simplified the smem iterator
...
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
...
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
...
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
...
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
...
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
...
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.
...
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
90ecd344ba
Merge branch 'master' into master_fixes. Merged up to master r375.
...
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
...
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
...
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
...
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
...
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
Heng Li
John Marshall
Rob Davies