Hi,
When we accidentally ran the 'use-modbam' mode with a BAM file without modification data, we get the following error:
ERROR: must be a methylation modification ('m')
It would be good to check for this condition, and generate a more complete and descriptive error to the effect of "Are you sure this is really a modbam file?"
Code location here:
https://github.com/huishenlab/biscuit/blame/2a00b8fee866142ea33835f6abce265b46dc0d62/src/epiread.c#L612
Our command (using UCSC hg38 fa):
biscuit epiread -@ 2 -M -b 0 -m 0 -a 0 -5 0 -3 0 -y 0.9 -L 100000 /mnt/input/Data/Genomes/hg38_noalt/hg38.analysisSet.fa.gz out.bam
out.bam.gz
Thanks!
Ben.