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

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, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads) Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.

Method Summary

Modifier and Type	Method and Description
void	acceptRecord(htsjdk.samtools.SAMRecord record) 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	setPerBaseOutput(java.io.File perBaseOutput) Sets the (optional) File to write per-base coverage information to.
void	setPerTargetOutput(java.io.File perTargetOutput) Sets the (optional) File to write per-target coverage information to.

Methods inherited from class java.lang.Object

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

Constructor Detail

PerUnitTargetMetricCollector

public 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,
                                    int minimumMappingQuality,
                                    int minimumBaseQuality,
                                    boolean clipOverlappingReads)

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)

Sets the (optional) File to write per-target coverage information to. If null (the default), no file is produced.

setPerBaseOutput

public void setPerBaseOutput(java.io.File perBaseOutput)

Sets the (optional) File to write per-base coverage information to. If null (the default), no file is produced.

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 record)

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:

record - 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