java.lang.Object
- picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector

All Implemented Interfaces:

PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>

Enclosing class:

AlignmentSummaryMetricsCollector
```
public class AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
extends Object
implements PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
```
Class that counts reads that match various conditions

Constructor Summary

Constructors
Constructor	Description
`IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category pairingCategory, String sample, String library, String readGroup)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`acceptRecord(SAMRecordAndReference samRecordAndReference)`	Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
`void`	`addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<AlignmentSummaryMetrics,Integer> file)`	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
`htsjdk.samtools.util.Histogram<Integer>`	`getAlignedReadHistogram()`
`AlignmentSummaryMetrics`	`getMetrics()`
`htsjdk.samtools.util.Histogram<Integer>`	`getReadHistogram()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - IndividualAlignmentSummaryMetricsCollector
```
public IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category pairingCategory,
                                                  String sample,
                                                  String library,
                                                  String readGroup)
```
- Method Detail
  - acceptRecord
```
public void acceptRecord(SAMRecordAndReference samRecordAndReference)
```
    Description copied from interface: PerUnitMetricCollector
    
    Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
    
    Specified by:
    
    acceptRecord in interface PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
    
    Parameters:
    
    samRecordAndReference - 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: PerUnitMetricCollector
    
    When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
    
    Specified by:
    
    finish in interface PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
  - addMetricsToFile
```
public void addMetricsToFile(htsjdk.samtools.metrics.MetricsFile<AlignmentSummaryMetrics,Integer> file)
```
    Description copied from interface: PerUnitMetricCollector
    
    Any metrics collected will be added to the metric file provided.
    
    Specified by:
    
    addMetricsToFile in interface PerUnitMetricCollector<AlignmentSummaryMetrics,Integer,SAMRecordAndReference>
    
    Parameters:
    
    file - MetricsFile to which all metrics created by this collector should be added
  - getMetrics
```
public AlignmentSummaryMetrics getMetrics()
```
  - getReadHistogram
```
public htsjdk.samtools.util.Histogram<Integer> getReadHistogram()
```
  - getAlignedReadHistogram
```
public htsjdk.samtools.util.Histogram<Integer> getAlignedReadHistogram()
```

Class AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

IndividualAlignmentSummaryMetricsCollector

Method Detail

acceptRecord

finish

addMetricsToFile

getMetrics

getReadHistogram

getAlignedReadHistogram