26b77eabef
updated version number
2011-10-21 12:32:00 -04:00
1cb409aaf2
use forward-only pac to reduce memory
2011-10-21 12:03:14 -04:00
fe9da3c704
allow to pac forward strand only
2011-10-21 10:57:12 -04:00
66629512d9
more carefully computed the availableWords
2011-10-20 23:49:03 -04:00
ec307a10e6
PE seems working; more testing needed
2011-10-20 17:45:41 -04:00
098f44cd51
nothing
2011-10-20 16:26:14 -04:00
156852b1dd
no change
2011-10-20 16:15:16 -04:00
2d2db5d50f
aln seems working
2011-10-20 16:13:35 -04:00
46123639cf
removed reverse pac; bwa is not working right now
2011-10-20 12:09:35 -04:00
b96f180a15
move bwt_gen/* to the root directory
2011-10-20 11:56:24 -04:00
70da24e177
restructure bns_fasta2bntseq() for further changes
2011-10-20 11:53:44 -04:00
b7e8c4c5aa
fixed a bug in 2occ4()
2011-10-20 11:23:23 -04:00
d6155ecf90
fixed a couple of gcc warnings
2011-10-19 17:45:27 -04:00
c948c647a0
make changes to bwt.c
2011-10-19 17:42:42 -04:00
b6d807b0b7
minor changes in case something goes wrong
2011-10-19 13:50:50 -04:00
1f02acbe09
added a few assertions
2011-10-19 00:26:56 -04:00
573ad0c98f
merge bwt_gen.h to bwt_gen.c
2011-10-18 23:48:46 -04:00
95b1ab7e96
first attempt to make bwt_gen work for >4GB seq
2011-10-18 23:41:26 -04:00
3114edcb7c
further code clean up
2011-10-18 16:41:44 -04:00
d2f357af3a
a little bit code clean up
2011-10-18 16:39:18 -04:00
d70754e234
update revision number
2011-10-14 10:32:31 -04:00
80e02281d5
minor change
2011-10-14 10:31:48 -04:00
2255c4cd4b
fixed a long existing bug
...
This bug may cause segfault (though never to me) and lead to missing
suboptimal hits. But the top hits should not be affected.
2011-10-12 00:05:01 -04:00
beedc988f0
Merge pull request #5 from tobiasmarschall/master
...
xa2multi.pl: reverse sequence and phred if orientations differ between primary and secondary alignment
2011-09-07 05:55:39 -07:00
3536e2113c
Bugfix: reverse (complement) sequence and phred string if alternative alignment has different orientation than primary alignment
2011-09-07 14:31:28 +02:00
4f7734eb97
Merge pull request #2 from RoelKluin/master
...
Filter Casava 1.8 flagged sequences with bwa aln -Y
2011-07-10 12:27:55 -07:00
db59a605d1
Remove sequences marked to be filtered by Casava-1.8 with bwa aln -Y
...
In Casava 1.8 the fastq output changed. e.g.
@EAS139:136:FC706VJ:2:5:1000:12850 1:Y:18:ATCACG
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
+
BBBBCCCC?<A?BC?7@@???????DBBA@@@@A@@
The part after the space, treated as comment by bwa, contains the fields:
<read number>:<is filtered>:<control number>:<barcode sequence>
With `Y' Casava indicates that a sequence should be filtered. This patch
enables bwa, with an -Y flag, to filter these sequences.
Signed-off-by: Roel Kluin <roel.kluin@gmail.com>
2011-07-10 17:04:06 +02:00
8f115a8e00
Revert "In Casava 1.8 the fastq output changed, the name had a space which bwa"
...
This reverts commit 36cd4f9882
2011-07-10 16:40:42 +02:00
36cd4f9882
In Casava 1.8 the fastq output changed, the name had a space which bwa
...
wasn't parsing correctly. This patch fixes that and enables bwa to filter
sequences marked by Casava, removing this tag from the output.
Signed-off-by: RoelKluin <roel.kluin@gmail.com>
2011-07-08 16:49:09 +02:00
d11674367d
convert XA to multiple lines
2011-06-09 18:08:49 -04:00
72563c38f3
automatically choose the algorithm for BWT
2011-06-09 17:33:25 -04:00
a74523a68d
increase maximum barcode length limit to 63bp
2011-06-09 17:17:13 -04:00
243e735431
applied patches from Alec Wysoker
2011-05-04 09:46:50 -04:00
4d064c69ce
added -s to ar
2011-05-04 09:41:30 -04:00
8d6b859bf8
speed up multi-threading
2011-04-07 17:26:08 -04:00
87664941b0
Release bwa-0.5.9 (r16)
2011-01-24 22:00:24 -05:00
7fd8948689
Added recommendation for PacBio reads
2011-01-22 13:20:11 -05:00
dac5395126
fixed a typo in help
2011-01-21 23:56:18 -05:00
0380cf02bf
update the manual page
2011-01-18 23:27:55 -05:00
1d7d8be9e8
Put BC: to both ends
2011-01-18 20:16:57 -05:00
51d354cd28
Added barcode support
2011-01-15 15:35:39 -05:00
10721ca602
Added an option to accept Illumina 1.3+ fastq
2011-01-15 14:07:08 -05:00
f335b33624
fixed a bug in bwase: no RG for unmapped read pairs
2011-01-15 10:32:45 -05:00
5b362b8718
Updated README
2011-01-13 21:38:37 -05:00
f85533c3c7
Updated README
2011-01-13 21:28:26 -05:00
ac93bbc6e4
Provided links to help information
2011-01-13 21:19:02 -05:00
94122ad6ee
Added a few others to .gitignore
2011-01-13 21:14:00 -05:00
fbedf6370b
Added .gitignore
2011-01-13 21:12:42 -05:00
5e30884730
Update to the latest modfication 0.5.9rc1-2. Update ChangeLog
2011-01-13 20:54:10 -05:00
007c3eb75d
Imported from my local bwa repository, the master repository.
2011-01-13 20:52:12 -05:00
Heng Li
Tobias Marschall
Roel Kluin