Open endrebak opened 7 years ago
I guess the best way of adding bam support would be to do the conversion before running the script with a warning that I think using bams instead of beds is suboptimal. If the conversion fails I'll throw an exception informing the user that the onus is on them to convert their wonky bam-files to bed.
My solution: if the input files are called path/to/file.bam
, create a file path/to/file.bed
. Do not delete it afterwards.
I think it is a bad idea for the below reasons. Feel free to suggest solutions: