71277f0fea
r896: more flexible ALT reading
2014-10-14 23:37:24 -04:00
2a18fa114f
r895: increase the default max_XA_hits_alt to 200
...
Because there are >100 HLA haplotypes
2014-10-14 16:58:42 -04:00
df20911110
r890: bns_intv2rid() may wrongly return -1
2014-10-14 14:49:53 -04:00
7b62fbb4ba
r880: bug in writing .ann file
2014-10-02 15:34:49 -04:00
a03d01f944
r878: XA is given to the best alignment
...
Non-ALT hits may get ALT hits in the XA tag. This will simplify haplotype
assignment.
2014-09-30 13:50:51 -04:00
0a2cf98293
r876: optionally ignore idxbase.alt file
2014-09-27 23:21:50 -04:00
dae4ca3ced
r875: invalid SAM output for ALT hits
2014-09-26 15:29:08 -04:00
7426a750ec
r868: use soft clip for ALT hits
2014-09-19 16:58:18 -04:00
9af36064e8
r867: fixed a few bugs; added ALT hits to XA
2014-09-19 16:50:21 -04:00
a41afe4c97
These files were committed on a wrong branch
2014-09-18 10:49:35 -04:00
a32d44d8d6
r855: show ALT hits in the PE mode, too
...
In the previous version, it does not
2014-09-17 23:07:56 -04:00
c982443210
r854: improved the calculation of pa
...
and build pa filtering into BWA-MEM
2014-09-17 16:26:28 -04:00
825ae92e58
r849: the pa tag now gives a number
...
... which is the ratio of this hit to the best ALT hit.
2014-09-17 13:05:35 -04:00
6f37c14f26
r848: tag alignments with primary ALT
2014-09-16 18:52:49 -04:00
a458442b24
r845: updated NEWS
...
I will use the new version for a while and then release it.
2014-09-16 14:38:41 -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
...
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
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
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
8d2b93156b
r821: more relax on containing seeds
2014-09-12 10:35:49 -04:00
f4aedddee6
r819: bugfix - added too many sub-SMEMs
2014-09-08 11:32:48 -04:00
35ac99b4f7
r815: optionally output ref fasta header
...
Also fixed a bug in reading .ann files
2014-08-29 10:51:23 -04:00
1e611b235c
r810: add err_puts()
...
puts() adds '\n', but fputs() does not.
2014-08-26 11:07:24 -04:00
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
...
For a very large reference genome, the default is too small.
2014-08-25 10:31:54 -04:00
705aa53894
Released 0.7.10
2014-07-13 22:57:27 -04:00
7fd6a11569
r788: segfault when the last ref is "weird"
...
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
...
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
...
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
8d2986ece2
r770: fixed a compiling warning
2014-05-14 14:44:03 -04:00
061c63f36a
r766: removed useless code
2014-05-13 13:09:29 -04:00
0168f39eeb
r765: fixed a declaration error
...
Reported by Andreas Tile from Debian
2014-05-13 12:54:23 -04:00
08517ac09b
r764: changed -c in "-x pacbio" to 500
2014-05-13 12:53:24 -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
cfe6996173
r760: removed commented code
...
It is slow and is not very effective. And I hate useless code.
2014-05-09 14:59:07 -04:00
43b498a37e
r759: bugfix - frac_rep not working
...
Also added commented code for a 3rd round seeding. Not used.
2014-05-09 14:56:59 -04:00
c9b33502f3
r758: fixed a typo
...
mostly negligible in practice
2014-05-07 15:07:29 -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
Heng Li