public static class CollectQualityYieldMetrics.QualityYieldMetricsCollector extends Object
| Modifier and Type | Field | Description |
|---|---|---|
boolean |
includeSupplementalAlignments |
| Constructor | Description |
|---|---|
QualityYieldMetricsCollector(boolean useOriginalQualities,
boolean includeSecondaryAlignments,
boolean includeSupplementalAlignments) |
| 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() |
public QualityYieldMetricsCollector(boolean useOriginalQualities,
boolean includeSecondaryAlignments,
boolean includeSupplementalAlignments)
public void acceptRecord(htsjdk.samtools.SAMRecord rec,
htsjdk.samtools.reference.ReferenceSequence ref)
public void finish()
public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics,Integer> metricsFile)