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