1. Check .sai versioning
2. Keep track of #ins and #del during backtrack
3. Use info above to get accurate aligned regions; don't call SW extension any more
4. Identify alignment crossing the for-rev boundary
5. Fixed a bug in printing the XA tag: ungapped alignments missing
stdaln.{c,h} was written ten years ago. Its local and SW extension code are
actually buggy (though that rarely happens and usually does not affect the
results too much). ksw.{c,h} is more concise, potentially faster, less buggy,
and richer in features.
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
Heng Li
Roel Kluin