Quip SAM parser crashes on some samples

[inumanag]

Quip crashes with segfault on the following file (with -a option): [ftp://ftp.sra.ebi.ac.uk/vol1/ERA242/ERA242167/bam/9827_2%2349.bam

Similar thing happens with the reference file (as a side note, by default this reference contains M character which confuses quip): ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz

I tried both dev and master branches, and both of them have the same problem. Running it through gdb gives me:

Program received signal SIGSEGV, Segmentation fault.
bam_calend (c=c@entry=0x6628a0, cigar=0x7bc951) at sam/bam.c:24
24          int op = cigar[k] & BAM_CIGAR_MASK;

Any ideas how to fix this?

Thank you!