Package picard.analysis
Class CollectWgsMetricsWithNonZeroCoverage
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.CollectWgsMetrics
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- picard.analysis.CollectWgsMetricsWithNonZeroCoverage
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@DocumentedFeature @ExperimentalFeature public class CollectWgsMetricsWithNonZeroCoverage extends CollectWgsMetrics
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
Metrics for evaluating the performance of whole genome sequencing experiments.protected class
CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
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Nested classes/interfaces inherited from class picard.analysis.CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection, CollectWgsMetrics.WgsMetricsCollector
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Field Summary
Fields Modifier and Type Field Description File
CHART_OUTPUT
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Fields inherited from class picard.analysis.CollectWgsMetrics
ALLELE_FRACTION, COUNT_UNPAIRED, COVERAGE_CAP, INCLUDE_BQ_HISTOGRAM, INPUT, intervalArugmentCollection, INTERVALS, LOCUS_ACCUMULATION_CAP, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, OUTPUT, READ_LENGTH, SAMPLE_SIZE, STOP_AFTER, THEORETICAL_SENSITIVITY_OUTPUT, USE_FAST_ALGORITHM
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectWgsMetricsWithNonZeroCoverage()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.protected WgsMetrics
generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram, int sampleSize)
protected CollectWgsMetrics.WgsMetricsCollector
getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)
CreatesAbstractWgsMetricsCollector
implementation according toCollectWgsMetrics.USE_FAST_ALGORITHM
value.protected htsjdk.samtools.SamReader
getSamReader()
Gets the SamReader from which records will be examined.-
Methods inherited from class picard.analysis.CollectWgsMetrics
getBasesExcludedBy, getIntervalsToExamine, getLocusIterator, getSamFileHeader, makeIntervalArgumentCollection, requiresReference
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Detail
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CHART_OUTPUT
@Argument(shortName="CHART", doc="A file (with .pdf extension) to write the chart to.") public File CHART_OUTPUT
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Method Detail
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getSamReader
protected htsjdk.samtools.SamReader getSamReader()
Description copied from class:CollectWgsMetrics
Gets the SamReader from which records will be examined. This will also set the header so that it is available in- Overrides:
getSamReader
in classCollectWgsMetrics
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Overrides:
doWork
in classCollectWgsMetrics
- Returns:
- program exit status.
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generateWgsMetrics
protected WgsMetrics generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram, int sampleSize)
- Overrides:
generateWgsMetrics
in classCollectWgsMetrics
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getCollector
protected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)
Description copied from class:CollectWgsMetrics
CreatesAbstractWgsMetricsCollector
implementation according toCollectWgsMetrics.USE_FAST_ALGORITHM
value.- Overrides:
getCollector
in classCollectWgsMetrics
- Parameters:
coverageCap
- the maximum depth/coverage to consider.intervals
- the intervals over which metrics are collected.- Returns:
- if
CollectWgsMetrics.USE_FAST_ALGORITHM
is enabled, returnsFastWgsMetricsCollector
implementation, otherwise default algorithm is used andCollectWgsMetrics.WgsMetricsCollector
is returned.
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