public static class CollectRawWgsMetrics.RawWgsMetrics extends CollectWgsMetrics.WgsMetrics
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
coverageCap, GENOME_TERRITORY, HET_SNP_Q, HET_SNP_SENSITIVITY, highQualityDepthHistogram, intervals, MAD_COVERAGE, MEAN_COVERAGE, MEDIAN_COVERAGE, PCT_100X, PCT_10X, PCT_15X, PCT_1X, PCT_20X, PCT_25X, PCT_30X, PCT_40X, PCT_50X, PCT_5X, PCT_60X, PCT_70X, PCT_80X, PCT_90X, PCT_EXC_BASEQ, PCT_EXC_CAPPED, PCT_EXC_DUPE, PCT_EXC_MAPQ, PCT_EXC_OVERLAP, PCT_EXC_TOTAL, PCT_EXC_UNPAIRED, SD_COVERAGE, theoreticalHetSensitivitySampleSize, unfilteredBaseQHistogram, unfilteredDepthHistogram
Constructor and Description |
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RawWgsMetrics() |
RawWgsMetrics(htsjdk.samtools.util.IntervalList intervals,
htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram,
htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram,
double pctExcludedByMapq,
double pctExcludedByDupes,
double pctExcludedByPairing,
double pctExcludedByBaseq,
double pctExcludedByOverlap,
double pctExcludedByCapping,
double pctTotal,
int coverageCap,
htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram,
int sampleSize) |
calculateDerivedFields, merge
canMerge, merge, mergeIfCan
public RawWgsMetrics()
public RawWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<java.lang.Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredDepthHistogram, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<java.lang.Integer> unfilteredBaseQHistogram, int sampleSize)