Package picard.analysis
Class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.analysis.MergeableMetricBase
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- picard.analysis.CollectWgsMetrics.WgsMetrics
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- picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
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- Enclosing class:
- CollectWgsMetricsWithNonZeroCoverage
public static class CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage extends CollectWgsMetrics.WgsMetrics
Metrics for evaluating the performance of whole genome sequencing experiments.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
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Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue
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Field Summary
Fields Modifier and Type Field Description CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
CATEGORY
One of either WHOLE_GENOME or NON_ZERO_REGIONS-
Fields inherited from class picard.analysis.CollectWgsMetrics.WgsMetrics
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
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Constructor Summary
Constructors Constructor 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)
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Method Summary
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Methods inherited from class picard.analysis.CollectWgsMetrics.WgsMetrics
calculateDerivedFields, merge
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Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, mergeIfCan
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Field Detail
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CATEGORY
public CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category CATEGORY
One of either WHOLE_GENOME or NON_ZERO_REGIONS
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Constructor Detail
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WgsMetricsWithNonZeroCoverage
public WgsMetricsWithNonZeroCoverage()
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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)
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