Package picard.analysis
Class AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
java.lang.Object
picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- 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
ConstructorsConstructorDescriptionIndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category pairingCategory, String sample, String library, String readGroup) -
Method Summary
Modifier and TypeMethodDescriptionvoidacceptRecord(SAMRecordAndReference samRecordAndReference) Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)voidaddMetricsToFile(htsjdk.samtools.metrics.MetricsFile<AlignmentSummaryMetrics, Integer> file) Any metrics collected will be added to the metric file provided.voidfinish()When all records have been collected, compute any final values needed to finish constructing metrics/Histogramhtsjdk.samtools.util.Histogram<Integer> htsjdk.samtools.util.Histogram<Integer>
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Constructor Details
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IndividualAlignmentSummaryMetricsCollector
public IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category pairingCategory, String sample, String library, String readGroup)
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Method Details
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acceptRecord
Description copied from interface:PerUnitMetricCollectorAdd a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)- Specified by:
acceptRecordin 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:PerUnitMetricCollectorWhen all records have been collected, compute any final values needed to finish constructing metrics/Histogram- Specified by:
finishin interfacePerUnitMetricCollector<AlignmentSummaryMetrics,Integer, SAMRecordAndReference>
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addMetricsToFile
public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<AlignmentSummaryMetrics, Integer> file) Description copied from interface:PerUnitMetricCollectorAny metrics collected will be added to the metric file provided.- Specified by:
addMetricsToFilein interfacePerUnitMetricCollector<AlignmentSummaryMetrics,Integer, SAMRecordAndReference> - Parameters:
file- MetricsFile to which all metrics created by this collector should be added
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getMetrics
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getReadHistogram
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getAlignedReadHistogram
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