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
58628ff263
first commit
2011-01-13 20:42:51 -05:00
Tobias Marschall
Heng Li
Roel Kluin