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fix: documentation errors in HsMetrics #1998

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fix: documentation errors in HsMetrics #1998

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9 changes: 5 additions & 4 deletions src/main/java/picard/analysis/directed/HsMetrics.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,8 +38,8 @@
* <li>Metrics that are intended for evaluating the performance of the wet-lab assay that generated the data.
* This group includes metrics like the number of bases mapping on/off/near baits, %selected, fold 80 base
* penalty, hs library size and the hs penalty metrics. These metrics are calculated prior to some of the
* filters are applied (e.g. low mapping quality reads, low base quality bases and bases overlapping in the middle
* of paired-end reads are all counted).
* filters are applied (e.g. duplicate reads, low mapping quality reads, low base quality bases and bases
* overlapping in the middle of paired-end reads are all counted).
* </li>
* <li>Metrics for assessing target coverage as a proxy for how well the data is likely to perform in downstream
* applications like variant calling. This group includes metrics like mean target coverage, the percentage of bases
Expand Down Expand Up @@ -82,10 +82,11 @@ public class HsMetrics extends PanelMetricsBase {
/** The mean coverage of all baits in the experiment. */
public double MEAN_BAIT_COVERAGE;

/** The number of aligned, de-duped, on-bait bases out of the PF bases available. */
/** The fraction of aligned, on-bait bases out of the PF bases available.
* (NOTE: This uses duplicate reads for both numerator and denominator) */
public double PCT_USABLE_BASES_ON_BAIT;

/** The number of aligned, de-duped, on-target bases out of all of the PF bases available. */
/** The fraction of aligned, de-duped, on-target bases out of all the PF bases available. */
public double PCT_USABLE_BASES_ON_TARGET;

/** The fold by which the baited region has been amplified above genomic background. */
Expand Down
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