Cigar ERROR

[avilella]

I am receiving errors from using readcount on a bam file aligned with bwa mem:

2017-03-31 11:26:05 bam_readcount STDERR ERROR (CigarRoller.cpp:127): Parsing CIGAR - invalid character found with parameter * and 0

Any ideas what may be wrong?

[pjvandehaar]

What command are you running?

[mktrost]

I don't think I'm familiar with bam_readcount. Is that a tool you are writing using libStatGen? (or am I just drawing a blank on this tool?)
Could it be that a read doesn't have a cigar? Such that the CIGAR string is just *. Potentially this error would come out if CigarRoller was trying to parse a cigar string of *. I'm not sure if it is an error in bam_readcount or libStatGen trying to parse an unknown cigar. I'd need more info on what was calling CigarRoller.