1bdd791539
r837: removed BAM support
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This is not necessary.
2014-09-16 09:57:35 -04:00
7244d66833
r836: a dangerous merge
2014-09-16 00:37:58 -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
43ce69104d
Removed PacBio read-to-read instruction
2014-09-15 23:59:35 -04:00
d013ea94b0
Removed instruction on ALT alignment
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Favoring the new method
2014-09-15 23:45:17 -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
41b137d202
Merge pull request #32 from mmoisse/patch-1
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Update example Illumina paired-end reads
2014-09-15 22:59:22 -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
8116bcc786
Merge branch 'dev' into alt
2014-09-14 15:40:52 -04:00
dfd8c9eeb6
Update README.md
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The 'Illumina paired-end reads no longer than ~70bp' example should use sampe instead of samse
2014-09-14 11:26:39 +02:00
8d2b93156b
r821: more relax on containing seeds
2014-09-12 10:35:49 -04:00
6739b713dd
Merge branch 'hotfix-utgaln' into dev
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Conflicts:
main.c
2014-09-08 12:44:42 -04:00
f4aedddee6
r819: bugfix - added too many sub-SMEMs
2014-09-08 11:32:48 -04:00
ca61fe3ad5
code backup
2014-09-08 08:52:02 -04:00
1934f0cf24
code backup
2014-09-05 13:20:52 -04:00
e4ad616d43
r816: read .alt file (not tested)
2014-09-05 12:49:50 -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
c7679ee781
Merge pull request #31 from jwbargsten/master
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wrong function to print @HD line in bwa_print_sam_hdr
2014-08-29 10:22:11 -04:00
9c5fd803e9
wrong function to print @HD line in bwa_print_sam_hdr
2014-08-29 11:51:07 +02:00
1e611b235c
r810: add err_puts()
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puts() adds '\n', but fputs() does not.
2014-08-26 11:07:24 -04:00
d9f654908f
Merge pull request #30 from mp15/header_hd
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Add @HD tag to SAM header
2014-08-26 09:44:29 -04:00
ec55ed8d83
Add @HD tag to SAM header
2014-08-26 12:06:16 +01:00
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
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For a very large reference genome, the default is too small.
2014-08-25 10:31:54 -04:00
1de61b556e
r806: polish BAM support
2014-08-08 13:36:56 -04:00
8a230db596
Merge branch 'nh_bam_support' of git://github.com/nh13/bwa into nh13-nh_bam_support
2014-08-08 13:12:54 -04:00
b73f4c977a
Merge branch 'master' into new-master
2014-08-07 21:51:58 -04:00
0a6f2660b4
Fixed a bug related to the score returned.
2014-08-07 13:50:42 -07:00
c1df343740
Merge branch 'master' of github.com:lh3/bwa
2014-08-07 13:49:01 -07:00
9bdcf31dec
don't process hard clipped SEQ
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The full read sequence has to be present.
2014-08-07 13:48:51 -07:00
a1a57d97be
r796: more debugging code
2014-08-07 14:58:51 -04:00
d9dfab2ba2
r795: intel's ksw_extend() replacement
2014-08-07 13:43:07 -04:00
b5415ba23d
first integration; compiled, but NOT TESTED!
2014-08-07 11:59:37 -04:00
5e56bec0f4
don't process hard clipped SEQ
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The full read sequence has to be present.
2014-08-07 10:36:28 -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
705aa53894
Released 0.7.10
2014-07-13 22:57:27 -04:00
7fd6a11569
r788: segfault when the last ref is "weird"
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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
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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
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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
Heng Li
mmoisse
Joachim Bargsten
Martin O. Pollard
Mustafa Ozdal
Nils Homer