picard.analysis.directed

Class TargetMetricsCollector.PerUnitTargetMetricCollector

java.lang.Object

picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector

All Implemented Interfaces:

PerUnitMetricCollector<METRIC_TYPE,java.lang.Integer,htsjdk.samtools.SAMRecord>

Enclosing class:

TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>

public class TargetMetricsCollector.PerUnitTargetMetricCollector
extends java.lang.Object
implements PerUnitMetricCollector<METRIC_TYPE,java.lang.Integer,htsjdk.samtools.SAMRecord>

Collect the Target Metrics for one unit of "accumulation" (i.e. for one sample, or for one library ...)

Constructor Summary

Constructors

Constructor and Description

TargetMetricsCollector.PerUnitTargetMetricCollector(java.lang.String probeSetName, java.util.Set<htsjdk.samtools.util.Interval> coverageTargets, java.lang.String sample, java.lang.String library, java.lang.String readGroup, long probeTerritory, long targetTerritory, long genomeSize, java.util.Map<htsjdk.samtools.util.Interval,java.lang.Double> intervalToGc) Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.

Method Summary

Methods

Modifier and Type	Method and Description
void	acceptRecord(htsjdk.samtools.SAMRecord rec) Adds information about an individual SAMRecord to the statistics.
void	addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<METRIC_TYPE,java.lang.Integer> hsMetricsComparableMetricsFile) 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
void	setBaitSetName(java.lang.String name) Sets the name of the bait set explicitly instead of inferring it from the bait file.
void	setPerTargetOutput(java.io.File perTargetOutput) If set, the metrics collector will output per target coverage information to this file.

Methods inherited from class java.lang.Object

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

Constructor Detail

TargetMetricsCollector.PerUnitTargetMetricCollector

public TargetMetricsCollector.PerUnitTargetMetricCollector(java.lang.String probeSetName,
                                                   java.util.Set<htsjdk.samtools.util.Interval> coverageTargets,
                                                   java.lang.String sample,
                                                   java.lang.String library,
                                                   java.lang.String readGroup,
                                                   long probeTerritory,
                                                   long targetTerritory,
                                                   long genomeSize,
                                                   java.util.Map<htsjdk.samtools.util.Interval,java.lang.Double> intervalToGc)

Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.

Method Detail

setPerTargetOutput

public void setPerTargetOutput(java.io.File perTargetOutput)

If set, the metrics collector will output per target coverage information to this file.

setBaitSetName

public void setBaitSetName(java.lang.String name)

Sets the name of the bait set explicitly instead of inferring it from the bait file.

acceptRecord

public void acceptRecord(htsjdk.samtools.SAMRecord rec)

Adds information about an individual SAMRecord to the statistics.

Specified by:

acceptRecord in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,java.lang.Integer,htsjdk.samtools.SAMRecord>

Parameters:

rec - 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<METRIC_TYPE extends MultilevelMetrics,java.lang.Integer,htsjdk.samtools.SAMRecord>

addMetricsToFile

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

Description copied from interface: PerUnitMetricCollector

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

Specified by:

addMetricsToFile in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,java.lang.Integer,htsjdk.samtools.SAMRecord>

Parameters:

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