public class AlignmentSummaryMetricsCollector extends SAMRecordAndReferenceMultiLevelCollector<AlignmentSummaryMetrics,java.lang.Comparable<?>>
UNKNOWN
Constructor and Description |
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AlignmentSummaryMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels,
java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
boolean doRefMetrics,
java.util.List<java.lang.String> adapterSequence,
int maxInsertSize,
java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations,
boolean isBisulfiteSequenced) |
Modifier and Type | Method and Description |
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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 record
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protected PerUnitMetricCollector<AlignmentSummaryMetrics,java.lang.Comparable<?>,SAMRecordAndReference> |
makeChildCollector(java.lang.String sample,
java.lang.String library,
java.lang.String readGroup)
Construct a PerUnitMetricCollector with the given arguments.
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makeArg
addAllLevelsToFile, finish, getAllReadsCollector, makeAllReadCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
public AlignmentSummaryMetricsCollector(java.util.Set<MetricAccumulationLevel> accumulationLevels, java.util.List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, boolean doRefMetrics, java.util.List<java.lang.String> adapterSequence, int maxInsertSize, java.util.Set<htsjdk.samtools.SamPairUtil.PairOrientation> expectedOrientations, boolean isBisulfiteSequenced)
protected PerUnitMetricCollector<AlignmentSummaryMetrics,java.lang.Comparable<?>,SAMRecordAndReference> makeChildCollector(java.lang.String sample, java.lang.String library, java.lang.String readGroup)
MultiLevelCollector
makeChildCollector
in class MultiLevelCollector<AlignmentSummaryMetrics,java.lang.Comparable<?>,SAMRecordAndReference>
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 collectorpublic void acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
MultiLevelCollector
acceptRecord
in class MultiLevelCollector<AlignmentSummaryMetrics,java.lang.Comparable<?>,SAMRecordAndReference>