Open hermidalc opened 1 year ago
I found the issue, Cedar does not work with SAM files (.sam or .sam.gz) and this is what's causing the segfault, even though it's documented to work with SAM files. If I provide a PAM equivalent alignment file it doesn't segfault and executes what looks to be correctly. Still, it should support PuffAligner SAM files, the source code looks like it does, but there's a bug somewhere.
I cannot seem to get Cedar to properly work without segfaulting. My input SAM is produced by PuffAligner against a CAMI example paired-end FASTQ and a Pufferfish index of 100 genomes. I'm using the Cedar
--flat
option. No matter what I try it always segfaults. @fataltes do you have any idea?