java.lang.Object
- picard.cmdline.CommandLineProgram
- - picard.analysis.CollectWgsMetrics
  - - picard.analysis.CollectWgsMetricsWithNonZeroCoverage

@DocumentedFeature
@ExperimentalFeature
public class CollectWgsMetricsWithNonZeroCoverage
extends CollectWgsMetrics

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`

Nested classes/interfaces inherited from class picard.analysis.CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection, CollectWgsMetrics.WgsMetrics, CollectWgsMetrics.WgsMetricsCollector

Field Summary

Fields
Modifier and Type Field Description

File CHART_OUTPUT
- 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
- Fields inherited from class picard.cmdline.CommandLineProgram
  COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors
Constructor Description

CollectWgsMetricsWithNonZeroCoverage()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected int`	`doWork()`	Do the work after command line has been parsed.
`protected CollectWgsMetrics.WgsMetrics`	`generateWgsMetrics(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)`
`protected CollectWgsMetrics.WgsMetricsCollector`	`getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals)`	Creates `AbstractWgsMetricsCollector` implementation according to {@link this#USE_FAST_ALGORITHM} value.
`protected htsjdk.samtools.SamReader`	`getSamReader()`	Gets the SamReader from which records will be examined.
`static void`	`main(String[] args)`

Methods inherited from class picard.analysis.CollectWgsMetrics
getBasesExcludedBy, getIntervalsToExamine, getLocusIterator, getSamFileHeader, makeIntervalArgumentCollection, requiresReference

Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

CHART_OUTPUT

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

Constructor Detail
- CollectWgsMetricsWithNonZeroCoverage
```
public CollectWgsMetricsWithNonZeroCoverage()
```

Method Detail

main

public static void main(String[] args)

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 class CollectWgsMetrics

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 CollectWgsMetrics.WgsMetrics generateWgsMetrics(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)

Overrides:: generateWgsMetrics in class CollectWgsMetrics

getCollector
```
protected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap,
                                                             htsjdk.samtools.util.IntervalList intervals)
```
Description copied from class: CollectWgsMetrics

Creates AbstractWgsMetricsCollector implementation according to {@link this#USE_FAST_ALGORITHM} value.

Overrides:

getCollector in class CollectWgsMetrics

Parameters:

coverageCap - the maximum depth/coverage to consider.

intervals - the intervals over which metrics are collected.

Returns:

if {@link this#USE_FAST_ALGORITHM} is enabled, returns FastWgsMetricsCollector implementation, otherwise default algorithm is used and CollectWgsMetrics.WgsMetricsCollector is returned.

Class CollectWgsMetricsWithNonZeroCoverage

Nested Class Summary

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

Field Summary

Fields inherited from class picard.analysis.CollectWgsMetrics

Fields inherited from class picard.cmdline.CommandLineProgram

Constructor Summary

Method Summary

Methods inherited from class picard.analysis.CollectWgsMetrics

Methods inherited from class picard.cmdline.CommandLineProgram

Methods inherited from class java.lang.Object

Field Detail

CHART_OUTPUT

Constructor Detail

CollectWgsMetricsWithNonZeroCoverage

Method Detail

main

getSamReader

doWork

generateWgsMetrics

getCollector