svtyper (https://github.com/cc2qe/svtyper) in order to get the genotype of some structural variants called using
Lumpy. Svtyper starts running and everything seems OK until it arrives to a specific variant of the input vcf file. At this record, svtyper crashes with the following error:
File "pysam/calignmentfile.pyx", line 836, in pysam.calignmentfile.AlignmentFile.mate (pysam/calignmentfile.c:10945) ValueError: mate not found
svtyper calls pysam at some point to get the mate pairs. I've read the code of pysam, and this is what I've found:
Throws a ValueError if read is unpaired or the mate is unmapped.
So, I think that svtyper crashes due to the presence of a read with unmapped mate supporting the SV. If this is the true reason of the error, does this make sense? I mean, I'm interested also in those reads which their mate is unmapped, this is a good pointer about the presence of a SV in that position, isn't it?