Picard HsMetrics module to show usable bases as percentages

[jamigo]

Description of bug:
PCT_USABLE_BASES_ON_BAIT and PCT_USABLE_BASES_ON_TARGET columns in Picard HsMetrics are being processed as bases rather than percentages by MultiQC.

MultiQC run details (please complete the following):

• Command used to run MultiQC: multiqc .
• MultiQC Version: MultiQC v1.9
• Operating System: Red Hat Enterprise Linux 7.5
• Python Version: Python 3.8.1
• Method of MultiQC installation: manual

Additional context
The issue is understandable, since Picard descriptions on these columns are:
"The number of aligned, de-duped, on-bait bases out of the PF bases available."
"The number of aligned, de-duped, on-target bases out of the PF bases available."
although these columns report percentages (values from 0 to 1) rather than number of bases (as one may deduct from the PCT_ column name).
https://broadinstitute.github.io/picard/javadoc/picard/picard/analysis/directed/HsMetrics.html

What works from me
I've edited HsMetrics.py module as follows, in case you want to consider something similar. I've included a few lines after line 277 to detect those columns and manually change their content:

            elif h.find("BASES") > -1:
                if h.startswith("PCT_USABLE"):
                    headers[h]['title'] = headers[h]['title'].replace("Pct u", "U")
                    headers[h]['modify'] = lambda x: x * 100
                    headers[h]['max'] = 100
                    headers[h]['suffix'] = '%'
                    headers[h]['shared_key'] = 'percentage'
                else:
                    headers[h]['title'] = "{} {}".format(config.base_count_prefix, headers[h]['title'])
                    headers[h]['modify'] = lambda x: x * config.base_count_multiplier
                    headers[h]['shared_key'] = 'base_count'

[ewels]

Great spot, thanks @jamigo!

I did a bit of extra tidying whilst I was digging around with the code, so hopefully a few of the column titles should look nicer now too.

Fixed in v1.10dev.

Phil