The Sage module was written to assume that the input alignment had a ".bam" and ".bam.bai" extension - which obviously doesn't hold if you have cram files as input. Rather than updating the input to include another CFG["inputs"]["bai"], which would require updates to existing run scripts that use Sage, I included a conditional "check if the .bai exists."
The Sage module was written to assume that the input alignment had a ".bam" and ".bam.bai" extension - which obviously doesn't hold if you have cram files as input. Rather than updating the input to include another
CFG["inputs"]["bai"], which would require updates to existing run scripts that use Sage, I included a conditional "check if the .bai exists."