The reference length should be checked against the length given in the BAM file #62
Description
I went to compare DamageProfiler with mapDamage output. I was surprised when mapDamage pointed out that the reference length differed from the number in the BAM file header and exited with an error. I had earlier made a plot with DamageProfiler, which did not complain. When I remapped the FASTQ and ran both programs, their outputs matched very closely.
DamageProfiler should definitely make this check. Its output was (unsurprisingly) very different when the BAM and reference were actually matching.