Package picard.analysis
Class CollectQualityYieldMetrics.QualityYieldMetricsCollector
- java.lang.Object
-
- picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
-
- Enclosing class:
- CollectQualityYieldMetrics
public static class CollectQualityYieldMetrics.QualityYieldMetricsCollector extends Object
-
-
Field Summary
Fields Modifier and Type Field Description boolean
includeSupplementalAlignments
-
Constructor Summary
Constructors Constructor Description QualityYieldMetricsCollector(boolean useOriginalQualities, boolean includeSecondaryAlignments, boolean includeSupplementalAlignments)
QualityYieldMetricsCollector(boolean useOriginalQualities, boolean includeSecondaryAlignments, boolean includeSupplementalAlignments, boolean flowMode)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
void
addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics,Integer> metricsFile)
void
finish()
-
-
-
Constructor Detail
-
QualityYieldMetricsCollector
public QualityYieldMetricsCollector(boolean useOriginalQualities, boolean includeSecondaryAlignments, boolean includeSupplementalAlignments)
-
QualityYieldMetricsCollector
public QualityYieldMetricsCollector(boolean useOriginalQualities, boolean includeSecondaryAlignments, boolean includeSupplementalAlignments, boolean flowMode)
-
-
Method Detail
-
acceptRecord
public void acceptRecord(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
-
finish
public void finish()
-
addMetricsToFile
public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics,Integer> metricsFile)
-
-