Package picard.analysis
Class AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
java.lang.Object
picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- All Implemented Interfaces:
PerUnitMetricCollector<AlignmentSummaryMetrics,Integer, SAMRecordAndReference>
- Enclosing class:
AlignmentSummaryMetricsCollector
public class AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
extends Object
implements PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
-
Constructor Summary
ConstructorsConstructorDescriptionGroupAlignmentSummaryMetricsPerUnitMetricCollector(String sample, String library, String readGroup) -
Method Summary
Modifier and TypeMethodDescriptionvoidAdd 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/Histogram
-
Constructor Details
-
GroupAlignmentSummaryMetricsPerUnitMetricCollector
-
-
Method Details
-
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:
args- Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously computed values that might be needed for this class
-
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>
-
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
-