For some reason the content of bam_files has been changed in recent iRAP updates, such that paired-end libraries return name-sorted bams from print_bam_filenames(), with single- end returning coordinate-sorted. This causes cram files generated by irap_single_lib to be name-sorted also, causing us problems in track generation.
This PR makes paired-end consistent with single-end, i.e. a coordinate-sorted bam.
For some reason the content of bam_files has been changed in recent iRAP updates, such that paired-end libraries return name-sorted bams from print_bam_filenames(), with single- end returning coordinate-sorted. This causes cram files generated by irap_single_lib to be name-sorted also, causing us problems in track generation.
This PR makes paired-end consistent with single-end, i.e. a coordinate-sorted bam.