org.broadinstitute.hellbender.metrics

Class InsertSizeMetricsCollector

java.lang.Object

org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector<InsertSizeMetrics,java.lang.Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs,PerUnitInsertSizeMetricsCollector>

org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollector

All Implemented Interfaces:

java.io.Serializable

public final class InsertSizeMetricsCollector
extends MultiLevelReducibleCollector<InsertSizeMetrics,java.lang.Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs,PerUnitInsertSizeMetricsCollector>
implements java.io.Serializable

Collects InsertSizeMetrics on the specified accumulationLevels

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
InsertSizeMetricsCollector()

Method Summary

Modifier and Type	Method and Description
InsertSizeMetricsCollector	combine(InsertSizeMetricsCollector target, InsertSizeMetricsCollector source) Combine two InsertSizeMetricsCollector objects and return a single InsertSizeMetricsCollector object representing the combined results.
PerUnitInsertSizeMetricsCollector	combineUnit(PerUnitInsertSizeMetricsCollector collector1, PerUnitInsertSizeMetricsCollector collector2) Combine two PerUnitInsertSizeMetricsCollector objects and return a single PerUnitInsertSizeMetricsCollector object representing the combined results.
void	finish(htsjdk.samtools.metrics.MetricsFile<InsertSizeMetrics,java.lang.Integer> metricsFile, java.lang.String inputName) Finish the metrics collection by saving any results to a metrics file.
java.util.List<ReadFilter>	getDefaultReadFilters() Return the read filter for InsertSizeMetrics collector.
void	initialize(InsertSizeMetricsArgumentCollection inputArgs, htsjdk.samtools.SAMFileHeader samHeader)
protected org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs	makeArg(htsjdk.samtools.SAMRecord samRecord, htsjdk.samtools.reference.ReferenceSequence refSeq) Convert the current SAMRecord and the ReferenceSequence for that record into an ARGTYPE object.
protected PerUnitInsertSizeMetricsCollector	makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup) Construct a PerUnitMetricCollector with the given arguments.

Methods inherited from class org.broadinstitute.hellbender.metrics.MultiLevelReducibleCollector

acceptRecord, addAllLevelsToFile, combine, 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

InsertSizeMetricsCollector

public InsertSizeMetricsCollector()

Method Detail

initialize

public void initialize(InsertSizeMetricsArgumentCollection inputArgs,
                       htsjdk.samtools.SAMFileHeader samHeader)

Parameters:

inputArgs - InsertSizeMetricsArgumentCollection populated with argument values. May not be null.

samHeader - samHeader for the input to be processed. May not be null.

getDefaultReadFilters

public java.util.List<ReadFilter> getDefaultReadFilters()

Return the read filter for InsertSizeMetrics collector.

Returns:

ReadFilter to be used to filter records

makeArg

protected org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs makeArg(htsjdk.samtools.SAMRecord samRecord,
                                                                                       htsjdk.samtools.reference.ReferenceSequence refSeq)

Description copied from class: MultiLevelReducibleCollector

Convert the current SAMRecord and the ReferenceSequence for that record into an ARGTYPE object. See method for use.

Specified by:

makeArg in class MultiLevelReducibleCollector<InsertSizeMetrics,java.lang.Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs,PerUnitInsertSizeMetricsCollector>

makeChildCollector

protected PerUnitInsertSizeMetricsCollector makeChildCollector(java.lang.String sample,
                                                               java.lang.String library,
                                                               java.lang.String readGroup)

Description copied from class: MultiLevelReducibleCollector

Construct a PerUnitMetricCollector with the given arguments.

Specified by:

makeChildCollector in class MultiLevelReducibleCollector<InsertSizeMetrics,java.lang.Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs,PerUnitInsertSizeMetricsCollector>

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

combine

public InsertSizeMetricsCollector combine(InsertSizeMetricsCollector target,
                                          InsertSizeMetricsCollector source)

Combine two InsertSizeMetricsCollector objects and return a single InsertSizeMetricsCollector object representing the combined results. NOTE: this implementation is destructive in that it merges the source into the target and returns the target as the combined object.

Parameters:

target - target destination of combined metrics. May not be null.

source - source of metrics to be combined into target. May not be null.

Returns:

single object representing the combined source and target objects

combineUnit

public PerUnitInsertSizeMetricsCollector combineUnit(PerUnitInsertSizeMetricsCollector collector1,
                                                     PerUnitInsertSizeMetricsCollector collector2)

Combine two PerUnitInsertSizeMetricsCollector objects and return a single PerUnitInsertSizeMetricsCollector object representing the combined results.

Specified by:

combineUnit in class MultiLevelReducibleCollector<InsertSizeMetrics,java.lang.Integer,org.broadinstitute.hellbender.metrics.InsertSizeMetricsCollectorArgs,PerUnitInsertSizeMetricsCollector>

Parameters:

collector1 - source PerUnitInsertSizeMetricsCollector. May not be null.

collector2 - target PerUnitInsertSizeMetricsCollector. May not be null.

Returns:

single PerUnitInsertSizeMetricsCollector object representing the combined source and target objects

finish

public void finish(htsjdk.samtools.metrics.MetricsFile<InsertSizeMetrics,java.lang.Integer> metricsFile,
                   java.lang.String inputName)

Finish the metrics collection by saving any results to a metrics file.

Parameters:

metricsFile - a metricsFile where the collected metrics should be stored. May not be null.

inputName - the name of the input, for optional inclusion in the metrics file. May not be null.