Package picard.analysis
Class GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
java.lang.Object
picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- All Implemented Interfaces:
PerUnitMetricCollector<GcBiasMetrics,
Integer, picard.analysis.GcBiasCollectorArgs>
- Enclosing class:
GcBiasMetricsCollector
public class GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
extends Object
implements PerUnitMetricCollector<GcBiasMetrics,Integer,picard.analysis.GcBiasCollectorArgs>
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Constructor Summary
ConstructorsConstructorDescriptionPerUnitGcBiasMetricsCollector
(String sample, String library, String readGroup) -
Method Summary
Modifier and TypeMethodDescriptionvoid
acceptRecord
(picard.analysis.GcBiasCollectorArgs args) Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)void
addMetricsToFile
(htsjdk.samtools.metrics.MetricsFile<GcBiasMetrics, 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
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Constructor Details
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PerUnitGcBiasMetricsCollector
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Method Details
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acceptRecord
public void acceptRecord(picard.analysis.GcBiasCollectorArgs 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 interfacePerUnitMetricCollector<GcBiasMetrics,
Integer, picard.analysis.GcBiasCollectorArgs> - Parameters:
args
- 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<GcBiasMetrics,
Integer, picard.analysis.GcBiasCollectorArgs>
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addMetricsToFile
Description copied from interface:PerUnitMetricCollector
Any metrics collected will be added to the metric file provided.- Specified by:
addMetricsToFile
in interfacePerUnitMetricCollector<GcBiasMetrics,
Integer, picard.analysis.GcBiasCollectorArgs> - Parameters:
file
- MetricsFile to which all metrics created by this collector should be added
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