.DepthOfCoverage_Target.txt has odd output

[vinjana]

The file ${sampleName}_${pid}_targetExtract.rmdup.bam.DepthOfCoverage_Target.txt is produced by the coverageQc D program and has somewhat odd output.

1. The normal chromosomes are expressed as overall coverage, i.e. all (non-N) positions in the genome are considered for both enumerator and denominator of the coverage value. That does not fit well to the "target"-specificity.
2. The "all" row in the output is restricted to the target regions, but because coverageQc is called on the complete file, instead of on the target-region specific file, the enumerator uses all bases (in- and off-target), while the denominator is the target regions size. If the target region size is not provided by the user to exclude Ns, then both enumerator and denominator are not as expected.

In a new version, make sure that these issues are fixed.