picard.analysis

Class GcBiasMetricsCollector

java.lang.Object

picard.metrics.MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>

picard.analysis.GcBiasMetricsCollector

public class GcBiasMetricsCollector
extends MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>

Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector

Field Summary

Fields inherited from class picard.metrics.MultiLevelCollector

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
GcBiasMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, int[] windowsByGc, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, int scanWindowSize, boolean bisulfite)

Method Summary

Modifier and Type	Method and Description
void	acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
protected picard.analysis.GcBiasCollectorArgs	makeArg(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
protected PerUnitMetricCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>	makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup) Construct a PerUnitMetricCollector with the given arguments.

Methods inherited from class picard.metrics.MultiLevelCollector

addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup

Methods inherited from class java.lang.Object

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

Constructor Detail

GcBiasMetricsCollector

public GcBiasMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
                              int[] windowsByGc,
                              java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                              int scanWindowSize,
                              boolean bisulfite)

Method Detail

makeArg

protected picard.analysis.GcBiasCollectorArgs makeArg(htsjdk.samtools.SAMRecord rec,
                                                      htsjdk.samtools.reference.ReferenceSequence ref)

Specified by:

makeArg in class MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>

makeChildCollector

protected PerUnitMetricCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs> makeChildCollector(java.lang.String sample,
                                                                                                                         java.lang.String library,
                                                                                                                         java.lang.String readGroup)

Description copied from class: MultiLevelCollector

Construct a PerUnitMetricCollector with the given arguments.

Specified by:

makeChildCollector in class MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>

Parameters:

sample - If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collector

library - If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collector

readGroup - If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector

Returns:

A PerUnitMetricCollector parameterized by the given arguments

acceptRecord

public void acceptRecord(htsjdk.samtools.SAMRecord rec,
                         htsjdk.samtools.reference.ReferenceSequence ref)

Description copied from class: MultiLevelCollector

Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record

Overrides:

acceptRecord in class MultiLevelCollector<GcBiasMetrics,java.lang.Integer,picard.analysis.GcBiasCollectorArgs>