Remove downsampling and filtering?

[iainrb]

In new versions of the bam-qc workflow, filtering and downsampling will be done upstream by other workflow tasks. So, the filtering/downsampling capabilities of bam-qc-metrics itself will no longer be used. We could:

• Remove the downsampling functionality from bam-qc-metrics to simplify code
• Remove output fields referring to filtering/downsampling results in bam-qc-metrics, to simplify output and reduce potential confusion. (Eg. "total reads", "unmapped reads".)

Low-priority, but could be useful. Should we do it?

[slazicoicr]

I am happy with either/both options. In my thinking, bam-qc should generate metrics for the input data and not modify it in any way (by filtering and down sampling). That way we have clear separation between data wrangling and metric reporting.

[iainrb]

Yes, I agree.

I'll make a ticket and put this on the TODO list. Probably won't be implemented on this iteration but we can do it when time allows.

[iainrb]

Ticket: https://jira.oicr.on.ca/browse/GP-2305