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Published 20 hours ago • verified publisher icon statgen

Cigar ERROR

Open avilella opened this issue 7 years ago • 2 comments

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?

avilella avatar Mar 31 '17 11:03 avilella

What command are you running?

pjvandehaar avatar Mar 31 '17 22:03 pjvandehaar

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.

mktrost avatar Mar 31 '17 22:03 mktrost