Package picard.analysis
Class AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- java.lang.Object
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- picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
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- All Implemented Interfaces:
PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
- Enclosing class:
- AlignmentSummaryMetricsCollector
public class AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector extends Object implements PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
Class that counts reads that match various conditions
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Constructor Summary
Constructors Constructor Description IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category pairingCategory, String sample, String library, String readGroup)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
acceptRecord(SAMRecordAndReference samRecordAndReference)
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)void
addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<AlignmentSummaryMetrics,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/Histogramhtsjdk.samtools.util.Histogram<Integer>
getAlignedReadHistogram()
AlignmentSummaryMetrics
getMetrics()
htsjdk.samtools.util.Histogram<Integer>
getReadHistogram()
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Constructor Detail
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IndividualAlignmentSummaryMetricsCollector
public IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category pairingCategory, String sample, String library, String readGroup)
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Method Detail
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acceptRecord
public void acceptRecord(SAMRecordAndReference samRecordAndReference)
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<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
- Parameters:
samRecordAndReference
- 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<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
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addMetricsToFile
public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<AlignmentSummaryMetrics,Integer> file)
Description copied from interface:PerUnitMetricCollector
Any metrics collected will be added to the metric file provided.- Specified by:
addMetricsToFile
in interfacePerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
- Parameters:
file
- MetricsFile to which all metrics created by this collector should be added
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getMetrics
public AlignmentSummaryMetrics getMetrics()
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getReadHistogram
public htsjdk.samtools.util.Histogram<Integer> getReadHistogram()
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getAlignedReadHistogram
public htsjdk.samtools.util.Histogram<Integer> getAlignedReadHistogram()
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