1bdd791539
r837: removed BAM support
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This is not necessary.
2014-09-16 09:57:35 -04:00
df09f38ad3
Merge branch 'dev'
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Conflicts:
README.md
bwamem.c
bwamem_pair.c
fastmap.c
main.c
2014-09-16 00:24:41 -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
1de61b556e
r806: polish BAM support
2014-08-08 13:36:56 -04:00
482a47a57e
adding support for SAM/BAM output using htslib. Please turn on within
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the Makefile.
2014-07-28 14:08:06 -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
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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
Heng Li
Nils Homer
John Marshall
Rob Davies