public abstract class TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> extends SAMRecordMultiLevelCollector<METRIC_TYPE,Integer>
Modifier and Type | Class and Description |
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static class |
TargetMetricsCollector.Coverage
A simple class that is used to store the coverage information about an interval.
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class |
TargetMetricsCollector.PerUnitTargetMetricCollector
Collect the Target Metrics for one unit of "accumulation" (i.e.
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UNKNOWN
Constructor and Description |
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TargetMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels,
List<SAMReadGroupRecord> samRgRecords,
ReferenceSequenceFile refFile,
File perTargetCoverage,
IntervalList targetIntervals,
IntervalList probeIntervals,
String probeSetName) |
Modifier and Type | Method and Description |
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abstract METRIC_TYPE |
convertMetric(picard.analysis.directed.TargetMetrics targetMetrics) |
protected PerUnitMetricCollector<METRIC_TYPE,Integer,SAMRecord> |
makeAllReadCollector() |
protected PerUnitMetricCollector<METRIC_TYPE,Integer,SAMRecord> |
makeChildCollector(String sample,
String library,
String readGroup)
Construct a PerUnitMetricCollector with the given arguments.
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protected static <MT extends MetricBase> |
reflectiveCopy(picard.analysis.directed.TargetMetrics targetMetrics,
MT outputMetrics,
String[] targetKeys,
String[] outputKeys)
Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics
to the outputMetrics' attributes of the same name.
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makeArg
acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
public TargetMetricsCollector(Set<MetricAccumulationLevel> accumulationLevels, List<SAMReadGroupRecord> samRgRecords, ReferenceSequenceFile refFile, File perTargetCoverage, IntervalList targetIntervals, IntervalList probeIntervals, String probeSetName)
public abstract METRIC_TYPE convertMetric(picard.analysis.directed.TargetMetrics targetMetrics)
protected static <MT extends MetricBase> void reflectiveCopy(picard.analysis.directed.TargetMetrics targetMetrics, MT outputMetrics, String[] targetKeys, String[] outputKeys)
MT
- The type of metric of outputMetricstargetMetrics
- A metric with values to be copiedoutputMetrics
- A metrics intended to receive values from targetMetricstargetKeys
- Specific names of attributes of targetMetrics to copy to outputMetrics, each key has a corresponding one in outputKeysoutputKeys
- Specific names of the destination attributes of outputMetrics that will be filled with values of outputMetrics, each key has a corresponding one in targetKeysprotected PerUnitMetricCollector<METRIC_TYPE,Integer,SAMRecord> makeChildCollector(String sample, String library, String readGroup)
MultiLevelCollector
makeChildCollector
in class MultiLevelCollector<METRIC_TYPE extends MultilevelMetrics,Integer,SAMRecord>
sample
- If aggregating by ALL_READS this will be null, otherwise the sample that will be used to identify
this collectorlibrary
- If aggregating by SAMPLE this will be null, otherwise the library that will be used to identify
this collectorreadGroup
- If aggregating by LIBRARY this will be null, otherwise the readGroup that will be used to identify
this collectorprotected PerUnitMetricCollector<METRIC_TYPE,Integer,SAMRecord> makeAllReadCollector()
makeAllReadCollector
in class MultiLevelCollector<METRIC_TYPE extends MultilevelMetrics,Integer,SAMRecord>