HsMetricCollector (picard 2.18.2 API)

java.lang.Object
- picard.metrics.MultiLevelCollector<BEAN,HKEY,htsjdk.samtools.SAMRecord>
- - picard.metrics.SAMRecordMultiLevelCollector<METRIC_TYPE,Integer>
  - - picard.analysis.directed.TargetMetricsCollector<HsMetrics>
    - - picard.analysis.directed.HsMetricCollector

```
public class HsMetricCollector
extends TargetMetricsCollector<HsMetrics>
```
Calculates HS metrics for a given SAM or BAM file. Requires the input of a list of target intervals and a list of bait intervals. Can be invoked either on an entire iterator of SAMRecords or be passed SAMRecords one at a time.

Nested Class Summary
- Nested classes/interfaces inherited from class picard.analysis.directed.TargetMetricsCollector
  TargetMetricsCollector.Coverage, TargetMetricsCollector.PerUnitTargetMetricCollector

Field Summary
- Fields inherited from class picard.metrics.MultiLevelCollector
  UNKNOWN
- Fields inherited from class picard.analysis.directed.TargetMetricsCollector
  NEAR_PROBE_DISTANCE_DEFAULT

Constructor Summary

Constructors
Constructor	Description
HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, boolean noSideEffects, int coverageCap, int sampleSize)
`HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels, List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords, htsjdk.samtools.reference.ReferenceSequenceFile refFile, File perTargetCoverage, File perBaseCoverage, htsjdk.samtools.util.IntervalList targetIntervals, htsjdk.samtools.util.IntervalList probeIntervals, String probeSetName, int nearProbeDistance, int minimumMappingQuality, int minimumBaseQuality, boolean clipOverlappingReads, int coverageCap, int sampleSize)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type Method Description

HsMetrics convertMetric(TargetMetrics targetMetrics)
- Methods inherited from class picard.metrics.MultiLevelCollector
  acceptRecord, addAllLevelsToFile, finish, getAllReadsCollector, makeLibraryCollector, makeReadGroupCollector, makeSampleCollector, setup
- Methods inherited from class java.lang.Object
  clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
- Methods inherited from class picard.metrics.SAMRecordMultiLevelCollector
  makeArg
- Methods inherited from class picard.analysis.directed.TargetMetricsCollector
  getNearProbeDistance, getNumBasesPassingMinimumBaseQuality, makeAllReadCollector, makeChildCollector, reflectiveCopy, setNearProbeDistance, setNoSideEffects

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`HsMetrics`	`convertMetric(TargetMetrics targetMetrics)`

Constructor Detail

HsMetricCollector

public HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels,
                         List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                         htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                         File perTargetCoverage,
                         File perBaseCoverage,
                         htsjdk.samtools.util.IntervalList targetIntervals,
                         htsjdk.samtools.util.IntervalList probeIntervals,
                         String probeSetName,
                         int nearProbeDistance,
                         int minimumMappingQuality,
                         int minimumBaseQuality,
                         boolean clipOverlappingReads,
                         int coverageCap,
                         int sampleSize)

HsMetricCollector

public HsMetricCollector(Set<MetricAccumulationLevel> accumulationLevels,
                         List<htsjdk.samtools.SAMReadGroupRecord> samRgRecords,
                         htsjdk.samtools.reference.ReferenceSequenceFile refFile,
                         File perTargetCoverage,
                         File perBaseCoverage,
                         htsjdk.samtools.util.IntervalList targetIntervals,
                         htsjdk.samtools.util.IntervalList probeIntervals,
                         String probeSetName,
                         int nearProbeDistance,
                         int minimumMappingQuality,
                         int minimumBaseQuality,
                         boolean clipOverlappingReads,
                         boolean noSideEffects,
                         int coverageCap,
                         int sampleSize)

Method Detail
- convertMetric
```
public HsMetrics convertMetric(TargetMetrics targetMetrics)
```
  Specified by:
  
  convertMetric in class TargetMetricsCollector<HsMetrics>

Class HsMetricCollector

Nested Class Summary

Nested classes/interfaces inherited from class picard.analysis.directed.TargetMetricsCollector

Field Summary

Fields inherited from class picard.metrics.MultiLevelCollector

Fields inherited from class picard.analysis.directed.TargetMetricsCollector

Constructor Summary

Method Summary

Methods inherited from class picard.metrics.MultiLevelCollector

Methods inherited from class java.lang.Object

Methods inherited from class picard.metrics.SAMRecordMultiLevelCollector

Methods inherited from class picard.analysis.directed.TargetMetricsCollector

Constructor Detail

HsMetricCollector

HsMetricCollector

Method Detail

convertMetric