public static class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage extends CollectWgsMetrics.WgsMetrics
| Modifier and Type | Class and Description |
|---|---|
static class |
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category |
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue| Modifier and Type | Field and Description |
|---|---|
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category |
CATEGORY
One of either WHOLE_GENOME or NON_ZERO_REGIONS
|
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 |
|---|
WgsMetricsWithNonZeroCoverage() |
WgsMetricsWithNonZeroCoverage(htsjdk.samtools.util.IntervalList intervals,
htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram,
htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram,
double pctExcludedByMapq,
double pctExcludedByDupes,
double pctExcludedByPairing,
double pctExcludedByBaseq,
double pctExcludedByOverlap,
double pctExcludedByCapping,
double pctTotal,
int coverageCap,
htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram,
int sampleSize) |
calculateDerivedFields, mergecanMerge, merge, mergeIfCanpublic CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category CATEGORY
public WgsMetricsWithNonZeroCoverage()
public WgsMetricsWithNonZeroCoverage(htsjdk.samtools.util.IntervalList intervals,
htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram,
htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram,
double pctExcludedByMapq,
double pctExcludedByDupes,
double pctExcludedByPairing,
double pctExcludedByBaseq,
double pctExcludedByOverlap,
double pctExcludedByCapping,
double pctTotal,
int coverageCap,
htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram,
int sampleSize)