trim_quality usage about bam-qc-metrics

[iainrb]

This issue has been superseded by code changes. The trim_quality parameter is now applied only once, using samtools view to create a "trimmed" BAM file which is then input to the stats calculations:

bam-qc-metrics/bam_qc_metrics/bam_qc.py

Line 44 in b86d16b

if self.trim_quality:

I think this is the behaviour we want, but if I'm mistaken please let me know.

[slazicoicr]

It would make sense to change the name of the parameter. To me, trim_quality implies that each read is being shortened based on quality. As samtools view is being used, this does not happen. The samtools docs has Skip alignments with MAPQ smaller than INT [0]., so maybe skip_below_mapq

[iainrb]

Yes, that makes sense. I'll rename the variable.

[iainrb]

Implemented in commit 7f3fd23