public class TargetMetricsCollector.PerUnitTargetMetricCollector extends Object implements PerUnitMetricCollector<METRIC_TYPE,Integer,SAMRecord>
Constructor and Description |
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TargetMetricsCollector.PerUnitTargetMetricCollector(String probeSetName,
Set<Interval> coverageTargets,
String sample,
String library,
String readGroup,
long probeTerritory,
long targetTerritory,
long genomeSize,
Map<Interval,Double> intervalToGc)
Constructor that parses the squashed reference to genome reference file and stores the
information in a map for later use.
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Modifier and Type | Method and Description |
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void |
acceptRecord(SAMRecord rec)
Adds information about an individual SAMRecord to the statistics.
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void |
addMetricsToFile(MetricsFile<METRIC_TYPE,Integer> hsMetricsComparableMetricsFile)
Any metrics collected will be added to the metric file provided.
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void |
finish()
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
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void |
setBaitSetName(String name)
Sets the name of the bait set explicitly instead of inferring it from the bait file.
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void |
setPerTargetOutput(File perTargetOutput)
If set, the metrics collector will output per target coverage information to this file.
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public TargetMetricsCollector.PerUnitTargetMetricCollector(String probeSetName, Set<Interval> coverageTargets, String sample, String library, String readGroup, long probeTerritory, long targetTerritory, long genomeSize, Map<Interval,Double> intervalToGc)
public void setPerTargetOutput(File perTargetOutput)
public void setBaitSetName(String name)
public void acceptRecord(SAMRecord rec)
acceptRecord
in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,Integer,SAMRecord>
rec
- Contains SAMRecord, SAMReadGroupRecord, ReferenceSequence of current record and any previously
computed values that might be needed for this classpublic void finish()
PerUnitMetricCollector
finish
in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,Integer,SAMRecord>
public void addMetricsToFile(MetricsFile<METRIC_TYPE,Integer> hsMetricsComparableMetricsFile)
PerUnitMetricCollector
addMetricsToFile
in interface PerUnitMetricCollector<METRIC_TYPE extends MultilevelMetrics,Integer,SAMRecord>
hsMetricsComparableMetricsFile
- MetricsFile to which all metrics created by this collector should be added