Open cerebis opened 7 years ago
As we require a bam file sorted by name, we should check this ourselves.
BWA adds a field to the header on the @HD line.
Eg. @HD VN:1.3 SO:queryname
@HD VN:1.3 SO:queryname
Pysam does not appear to offer this check as a method call. Possibly aligner dependent.
We can also simply check the file for conflicting alphanumeric order, as we go through it.
As we require a bam file sorted by name, we should check this ourselves.
BWA adds a field to the header on the @HD line.
Eg.
@HD VN:1.3 SO:querynamePysam does not appear to offer this check as a method call. Possibly aligner dependent.
We can also simply check the file for conflicting alphanumeric order, as we go through it.