FastWgsMetricsCollector (picard 2.18.25 API)

java.lang.Object
- picard.analysis.AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
- - picard.analysis.FastWgsMetricsCollector

```
public class FastWgsMetricsCollector
extends AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
```
Class represents fast algorithm for collecting data from AbstractLocusInfo with a list of aligned EdgingRecordAndOffset objects. According to the algorithm we receive only two EdgingRecordAndOffset objects for each alignment block of a read: one for the start of block and one for the end. When meeting a EdgingRecordAndOffset with type EdgingRecordAndOffset.Type.BEGIN, all information from the alignment block is accumulated in the collector, read name is added to a map holding the names of processed reads for detecting overlapping positions. When meeting a EdgingRecordAndOffset with type EdgingRecordAndOffset.Type.END, the read name is removed from the map with names of processed reads.

Field Summary
- Fields inherited from class picard.analysis.AbstractWgsMetricsCollector
  counter, coverageCap, highQualityDepthHistogramArray, intervals, unfilteredBaseQHistogramArray, unfilteredDepthHistogramArray

Constructor Summary

Constructors
Constructor	Description
`FastWgsMetricsCollector(CollectWgsMetrics collectWgsMetrics, int coverageCap, htsjdk.samtools.util.IntervalList intervals)`	Creates a collector and initializes the inner data structures

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.EdgingRecordAndOffset> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN)`	Accumulates the data from AbstractLocusInfo in inner structures

Methods inherited from class picard.analysis.AbstractWgsMetricsCollector
addBaseQHistogram, addToMetricsFile, getHighQualityDepthHistogram, getHistogram, getMetrics, getUnfilteredBaseQHistogram, getUnfilteredDepthHistogram, setCounter

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

- Constructor Detail
  - FastWgsMetricsCollector
```
public FastWgsMetricsCollector(CollectWgsMetrics collectWgsMetrics,
                               int coverageCap,
                               htsjdk.samtools.util.IntervalList intervals)
```
    Creates a collector and initializes the inner data structures
    
    Parameters:
    
    collectWgsMetrics - CollectWgsMetrics, that creates this collector
    
    coverageCap - coverage cap
- Method Detail
  - addInfo
```
public void addInfo(htsjdk.samtools.util.AbstractLocusInfo<htsjdk.samtools.util.EdgingRecordAndOffset> info,
                    htsjdk.samtools.reference.ReferenceSequence ref,
                    boolean referenceBaseN)
```
    Description copied from class: AbstractWgsMetricsCollector
    
    Accumulates the data from AbstractLocusInfo in inner structures
    
    Specified by:
    
    addInfo in class AbstractWgsMetricsCollector<htsjdk.samtools.util.EdgingRecordAndOffset>
    
    Parameters:
    
    info - AbstractLocusInfo with aligned to reference position reads
    
    ref - ReferenceSequence
    
    referenceBaseN - true if current the value of reference base represents a no call