Using Pysam to extract paired reads
I am using Pysam to process a bam file containing paired reads. However, I get the error
AttributeError: 'csamtools.AlignedRead' object has no attribute 'rnext'
when I try to extract the chromosome that the mate of a read is aligned to. What am I doing wrong?
for row in samfile:
print(samfile.getrname(row.rname)+' '+samfile.getrname(row.rnext))
It gives the read's reference properly, however it gives an error for the mate's reference.
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There are known issues with insufficient documentation for pysam. If you are comfortable with perl, you can try Bio::DB::Sam instead. It will do the same job with enough documentation for troubleshooting.