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>
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>
Heng Li
Roel Kluin