Segfault on extracthairs

[klannert]

I'm trying to run HapCUT2 on a single-sample VCF, not an especially large one (3184 variants). ExtractHAIRS chokes midway and gives a segfault:

reading sorted bamfile VWDSeq_215.bam
processing reads mapped to chrom "chr1"
processing reads mapped to chrom "chr2"
cleaning buffer for prev chrom fragments 219
Segmentation fault: 11

Running this on MacOS 11.4.

[vibansal]

Which version of HapCUT2 are you using (it will help figure out if the problem is due to a recent change)? Also, does ExtractHAIRS work on other datasets that you may have analyzed? Thanks.

[klannert]

This install is v1.3.1, and this is my first time running this version on this OS. I have an older version working well on a machine with MacOS 10.14.7, I think that one is running HapCUT2 v1.2.