Fold80 Bug Fix

[Patrick-Schlaeger-Broad]

Description

Added highQualityDepthHistogramNonZero as a histogram variable to WgsMetrics.java and CollectTargetMetrics.java.highQualityDepthHistogramNonZero is identical to highQualityDepthHistogram, but gets rid of its '0 coverage' bin. highQualityDepthHistogramNonZero is then used in the place of the highQualityDepthHistogram for the calculation of the FOLD_80_BASE_PENALTY metric. The motivation for making this change is to have these metrics accurately calculate the FOLD_80_BASE_PENALTY metric accord to its definition: "The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets."

This change fixes the issue brought up in the following Picard Bug Report.

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