AbstractWgsMetricsCollector (picard 2.18.2 API)

java.lang.Object
- picard.analysis.AbstractWgsMetricsCollector<T>

Direct Known Subclasses:

CollectWgsMetrics.WgsMetricsCollector, FastWgsMetricsCollector
```
public abstract class AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset>
extends Object
```
Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
The shared code for forming result for CollectWgsMetrics is abstracted into this class. Classes that extend this collector implement their logic in addInfo() method.

Field Summary

Fields
Modifier and Type	Field	Description
`protected long`	`counter`	The number of processed genomic bases
`protected int`	`coverageCap`	Positions with coverage exceeding this value are treated as if they had coverage at this value
`protected long[]`	`highQualityDepthHistogramArray`	Count of sites with a given depth of coverage.
`protected htsjdk.samtools.util.IntervalList`	`intervals`
`protected long[]`	`unfilteredBaseQHistogramArray`	Count of bases observed with a given base quality.
`protected long[]`	`unfilteredDepthHistogramArray`	Count of sites with a given depth of coverage.

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method	Description
`protected void`	`addBaseQHistogram(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file)`
`abstract void`	`addInfo(htsjdk.samtools.util.AbstractLocusInfo<T> info, htsjdk.samtools.reference.ReferenceSequence ref, boolean referenceBaseN)`	Accumulates the data from AbstractLocusInfo in inner structures
`void`	`addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file, boolean includeBQHistogram, CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)`	Adds collected metrics and depth histogram to file
`protected htsjdk.samtools.util.Histogram<Integer>`	`getHighQualityDepthHistogram()`
`protected htsjdk.samtools.util.Histogram<Integer>`	`getHistogram(long[] array, String binLabel, String valueLabel)`
`protected CollectWgsMetrics.WgsMetrics`	`getMetrics(CountingFilter dupeFilter, CountingFilter mapqFilter, CountingPairedFilter pairFilter)`	Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
`protected htsjdk.samtools.util.Histogram<Integer>`	`getUnfilteredBaseQHistogram()`
`protected htsjdk.samtools.util.Histogram<Integer>`	`getUnfilteredDepthHistogram()`
`void`	`setCounter(long counter)`	Sets the counter to the current number of processed loci.

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

Field Detail
- unfilteredDepthHistogramArray
```
protected final long[] unfilteredDepthHistogramArray
```
  Count of sites with a given depth of coverage. Includes all but quality 2 bases. We draw depths from this histogram when we calculate the theoretical het sensitivity.
- unfilteredBaseQHistogramArray
```
protected final long[] unfilteredBaseQHistogramArray
```
  Count of bases observed with a given base quality. Includes all but quality 2 bases. We draw bases from this histogram when we calculate the theoretical het sensitivity.
- highQualityDepthHistogramArray
```
protected final long[] highQualityDepthHistogramArray
```
  Count of sites with a given depth of coverage. Excludes bases with quality below MINIMUM_BASE_QUALITY (default 20).
- coverageCap
```
protected final int coverageCap
```
  Positions with coverage exceeding this value are treated as if they had coverage at this value
- intervals
```
protected final htsjdk.samtools.util.IntervalList intervals
```
- counter
```
protected long counter
```
  The number of processed genomic bases

Method Detail

addInfo
```
public abstract void addInfo(htsjdk.samtools.util.AbstractLocusInfo<T> info,
                             htsjdk.samtools.reference.ReferenceSequence ref,
                             boolean referenceBaseN)
```
Accumulates the data from AbstractLocusInfo in inner structures

Parameters:

info - AbstractLocusInfo with aligned to reference position reads

ref - ReferenceSequence

referenceBaseN - true if current the value of reference base represents a no call

addToMetricsFile

public void addToMetricsFile(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file,
                             boolean includeBQHistogram,
                             CountingFilter dupeFilter,
                             CountingFilter mapqFilter,
                             CountingPairedFilter pairFilter)

Adds collected metrics and depth histogram to file

Parameters:: file - MetricsFile for result of collector's work; dupeFilter - counting filter for duplicate reads; mapqFilter - counting filter for mapping quality; pairFilter - counting filter for reads without a mapped mate pair

addBaseQHistogram

protected void addBaseQHistogram(htsjdk.samtools.metrics.MetricsFile<CollectWgsMetrics.WgsMetrics,Integer> file)

getHighQualityDepthHistogram

protected htsjdk.samtools.util.Histogram<Integer> getHighQualityDepthHistogram()

getUnfilteredDepthHistogram

protected htsjdk.samtools.util.Histogram<Integer> getUnfilteredDepthHistogram()

getUnfilteredBaseQHistogram

protected htsjdk.samtools.util.Histogram<Integer> getUnfilteredBaseQHistogram()

getHistogram

protected htsjdk.samtools.util.Histogram<Integer> getHistogram(long[] array,
                                                               String binLabel,
                                                               String valueLabel)

getMetrics

protected CollectWgsMetrics.WgsMetrics getMetrics(CountingFilter dupeFilter,
                                                  CountingFilter mapqFilter,
                                                  CountingPairedFilter pairFilter)

Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics

Parameters:: dupeFilter - counting filter for duplicate reads; mapqFilter - counting filter for mapping quality; pairFilter - counting filter for reads without a mapped mate pair
Returns:: CollectWgsMetrics.WgsMetrics with set fields

setCounter
```
public void setCounter(long counter)
```
Sets the counter to the current number of processed loci. Counter, must be updated from outside, since we are skipping a no call reference positions outside of the collector

Parameters:

counter - number of processed loci

Class AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset>

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

unfilteredDepthHistogramArray

unfilteredBaseQHistogramArray

highQualityDepthHistogramArray

coverageCap

intervals

counter

Method Detail

addInfo

addToMetricsFile

addBaseQHistogram

getHighQualityDepthHistogram

getUnfilteredDepthHistogram

getUnfilteredBaseQHistogram

getHistogram

getMetrics

setCounter