picard.analysis.directed

Class InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector

java.lang.Object

picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector

All Implemented Interfaces:

PerUnitMetricCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

Enclosing class:

InsertSizeMetricsCollector

public class InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
extends java.lang.Object
implements PerUnitMetricCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)

Constructor Summary

Constructors

Constructor and Description
PerUnitInsertSizeMetricsCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup)

Method Summary

Modifier and Type	Method and Description
void	acceptRecord(picard.analysis.directed.InsertSizeCollectorArgs args) Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
void	addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<InsertSizeMetrics,java.lang.Integer> file) Any metrics collected will be added to the metric file provided.
void	finish() When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
double	getTotalInserts()

Methods inherited from class java.lang.Object

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

Constructor Detail

PerUnitInsertSizeMetricsCollector

public PerUnitInsertSizeMetricsCollector(java.lang.String sample,
                                         java.lang.String library,
                                         java.lang.String readGroup)

Method Detail

acceptRecord

public void acceptRecord(picard.analysis.directed.InsertSizeCollectorArgs args)

Description copied from interface: PerUnitMetricCollector

Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)

Specified by:

acceptRecord in interface PerUnitMetricCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

Parameters:

args - Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously computed values that might be needed for this class

finish

public void finish()

Description copied from interface: PerUnitMetricCollector

When all records have been collected, compute any final values needed to finish constructing metrics/Histogram

Specified by:

finish in interface PerUnitMetricCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

getTotalInserts

public double getTotalInserts()

addMetricsToFile

public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<InsertSizeMetrics,java.lang.Integer> file)

Description copied from interface: PerUnitMetricCollector

Any metrics collected will be added to the metric file provided.

Specified by:

addMetricsToFile in interface PerUnitMetricCollector<InsertSizeMetrics,java.lang.Integer,picard.analysis.directed.InsertSizeCollectorArgs>

Parameters:

file - MetricsFile to which all metrics created by this collector should be added