picard.analysis

Class CollectWgsMetricsWithNonZeroCoverage

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.CollectWgsMetrics

picard.analysis.CollectWgsMetricsWithNonZeroCoverage

public class CollectWgsMetricsWithNonZeroCoverage
extends CollectWgsMetrics

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage Metrics for evaluating the performance of whole genome sequencing experiments.
protected class	CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector

Nested classes/interfaces inherited from class picard.analysis.CollectWgsMetrics

CollectWgsMetrics.WgsMetrics, CollectWgsMetrics.WgsMetricsCollector

Field Summary

Fields

Modifier and Type	Field and Description
java.io.File	CHART_OUTPUT

Fields inherited from class picard.analysis.CollectWgsMetrics

COUNT_UNPAIRED, COVERAGE_CAP, INCLUDE_BQ_HISTOGRAM, INPUT, INTERVALS, LOCUS_ACCUMULATION_CAP, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, OUTPUT, REFERENCE_SEQUENCE, SAMPLE_SIZE, STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectWgsMetricsWithNonZeroCoverage()

Method Summary

Modifier and Type	Method and Description
protected int	doWork() Do the work after command line has been parsed.
protected CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage	generateWgsMetrics()
protected CollectWgsMetrics.WgsMetricsCollector	getCollector(int coverageCap)
static void	main(java.lang.String[] args)

Methods inherited from class picard.analysis.CollectWgsMetrics

getBasesExcludedBy, getLocusIterator, getSamFileHeader

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CHART_OUTPUT

@Option(shortName="CHART",
        doc="A file (with .pdf extension) to write the chart to.")
public java.io.File CHART_OUTPUT

Constructor Detail

CollectWgsMetricsWithNonZeroCoverage

public CollectWgsMetricsWithNonZeroCoverage()

Method Detail

main

public static void main(java.lang.String[] args)

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 class CollectWgsMetrics

Returns:

program exit status.

generateWgsMetrics

protected CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage generateWgsMetrics()

Overrides:

generateWgsMetrics in class CollectWgsMetrics

getCollector

protected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap)

Overrides:

getCollector in class CollectWgsMetrics