picard.sam.SamErrorMetric

Class ReadBaseStratification.GCContentStratifier

java.lang.Object

picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier

All Implemented Interfaces:

ReadBaseStratification.RecordAndOffsetStratifier<java.lang.Double>

Enclosing class:

ReadBaseStratification

public static class ReadBaseStratification.GCContentStratifier
extends java.lang.Object

A stratifier that uses GC (of the read) to stratify. Since the reads are expected to be seen over and over again, the GC is cached

Stratification happens into (integer) percents.

Constructor Summary

Constructors

Constructor and Description
GCContentStratifier()

Method Summary

Modifier and Type	Method and Description
java.lang.String	getSuffix()
T	stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset, htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)
java.lang.Double	stratify(htsjdk.samtools.SAMRecord sam)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

GCContentStratifier

public GCContentStratifier()

Method Detail

stratify

public java.lang.Double stratify(htsjdk.samtools.SAMRecord sam)

getSuffix

public java.lang.String getSuffix()

stratify

public T stratify(htsjdk.samtools.util.SamLocusIterator.RecordAndOffset recordAndOffset,
                  htsjdk.samtools.reference.SamLocusAndReferenceIterator.SAMLocusAndReference locusInfo)

Specified by:

stratify in interface ReadBaseStratification.RecordAndOffsetStratifier<T extends java.lang.Comparable<T>>