Package picard.analysis.directed
Class TargetMetricsCollector.PerUnitTargetMetricCollector
java.lang.Object
picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
- All Implemented Interfaces:
PerUnitMetricCollector<METRIC_TYPE,
Integer, htsjdk.samtools.SAMRecord>
- Enclosing class:
TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics>
public class TargetMetricsCollector.PerUnitTargetMetricCollector
extends Object
implements PerUnitMetricCollector<METRIC_TYPE,Integer,htsjdk.samtools.SAMRecord>
Collect the Target Metrics for one unit of "accumulation" (i.e. for one sample, or for one library ...)
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Constructor Summary
ConstructorsConstructorDescriptionPerUnitTargetMetricCollector
(String probeSetName, Set<htsjdk.samtools.util.Interval> coverageTargets, String sample, String library, String readGroup, long probeTerritory, long targetTerritory, long genomeSize, Map<htsjdk.samtools.util.Interval, Double> intervalToGc, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean includeIndels) Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use. -
Method Summary
Modifier and TypeMethodDescriptionvoid
acceptRecord
(htsjdk.samtools.SAMRecord record) Adds information about an individual SAMRecord to the statistics.void
addMetricsToFile
(htsjdk.samtools.metrics.MetricsFile<METRIC_TYPE, 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/HistogramMap
<htsjdk.samtools.util.Interval, TargetMetricsCollector.Coverage> Returns the accumulated coverage per target.void
setBaitSetName
(String name) Sets the name of the bait set explicitly instead of inferring it from the bait file.void
setPerBaseOutput
(File perBaseOutput) Sets the (optional) File to write per-base coverage information to.void
setPerTargetOutput
(File perTargetOutput) Sets the (optional) File to write per-target coverage information to.
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Constructor Details
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PerUnitTargetMetricCollector
public PerUnitTargetMetricCollector(String probeSetName, Set<htsjdk.samtools.util.Interval> coverageTargets, String sample, String library, String readGroup, long probeTerritory, long targetTerritory, long genomeSize, Map<htsjdk.samtools.util.Interval, Double> intervalToGc, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean includeIndels) Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
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Method Details
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setPerTargetOutput
Sets the (optional) File to write per-target coverage information to. If null (the default), no file is produced. -
setPerBaseOutput
Sets the (optional) File to write per-base coverage information to. If null (the default), no file is produced. -
setBaitSetName
Sets the name of the bait set explicitly instead of inferring it from the bait file. -
getCoverageByTarget
Returns the accumulated coverage per target. Note that while the returned Map is immutable, it is possible that the underlying Map will continue to be mutated if the map is retrieved prior to additional calls toacceptRecord(SAMRecord)
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acceptRecord
public void acceptRecord(htsjdk.samtools.SAMRecord record) Adds information about an individual SAMRecord to the statistics.- Specified by:
acceptRecord
in interfacePerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,
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
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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 interfacePerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,
Integer, htsjdk.samtools.SAMRecord>
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addMetricsToFile
public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<METRIC_TYPE, Integer> hsMetricsComparableMetricsFile) Description copied from interface:PerUnitMetricCollector
Any metrics collected will be added to the metric file provided.- Specified by:
addMetricsToFile
in interfacePerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,
Integer, htsjdk.samtools.SAMRecord> - Parameters:
hsMetricsComparableMetricsFile
- MetricsFile to which all metrics created by this collector should be added
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