mipgen_smmip_collapser.py generating SAM with empty CIGAR

[Kasia Kedzierska]

Hi,

I tried to run the mipgen_smmip_collapser.py on some of my samples. Unfortunately, the output (collapsed.all_reads.unique.sam) is corrupted. I managed to trace it to (at least) one read being reported with CIGAR, SEQ and QUAL fields empty, and the POS different that the same read in the input file. I run ValidateSamFile on the input and it seems to be ok (except not having a read group, but that had not been a problem with other files).

Any idea what is causing this? Or how to further debug it?

Would very much appreciate any suggestions.