Package picard.analysis
Class AlignmentSummaryMetricsCollector
- java.lang.Object
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- picard.metrics.MultiLevelCollector<BEAN,HKEY,SAMRecordAndReference>
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- picard.metrics.SAMRecordAndReferenceMultiLevelCollector<AlignmentSummaryMetrics,Comparable<?>>
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- picard.analysis.AlignmentSummaryMetricsCollector
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public class AlignmentSummaryMetricsCollector extends SAMRecordAndReferenceMultiLevelCollector<AlignmentSummaryMetrics,Comparable<?>>
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Field Summary
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Fields inherited from class picard.metrics.MultiLevelCollector
UNKNOWN
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Constructor Summary
Constructors Constructor Description AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, boolean doRefMetrics, List<String> adapterSequence, int maxInsertSize, Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, boolean isBisulfiteSequenced)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this recordprotected PerUnitMetricCollector<AlignmentSummaryMetrics,Comparable<?>,SAMRecordAndReference>
makeChildCollector(String sample, String library, String readGroup)
Construct a PerUnitMetricCollector with the given arguments.-
Methods inherited from class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
makeArg
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Methods inherited from class picard.metrics.MultiLevelCollector
addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
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Constructor Detail
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AlignmentSummaryMetricsCollector
public AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, boolean doRefMetrics, List<String> adapterSequence, int maxInsertSize, Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, boolean isBisulfiteSequenced)
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Method Detail
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makeChildCollector
protected PerUnitMetricCollector<AlignmentSummaryMetrics,Comparable<?>,SAMRecordAndReference> makeChildCollector(String sample, String library, String readGroup)
Description copied from class:MultiLevelCollector
Construct a PerUnitMetricCollector with the given arguments.- Specified by:
makeChildCollector
in classMultiLevelCollector<AlignmentSummaryMetrics,Comparable<?>,SAMRecordAndReference>
- Parameters:
sample
- If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify this collectorlibrary
- If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify this collectorreadGroup
- If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify this collector- Returns:
- A PerUnitMetricCollector parameterized by the given arguments
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acceptRecord
public void acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
Description copied from class:MultiLevelCollector
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record- Overrides:
acceptRecord
in classMultiLevelCollector<AlignmentSummaryMetrics,Comparable<?>,SAMRecordAndReference>
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