picard.sam.SamErrorMetric

Class ReadBaseStratification.LongShortHomopolymerStratifier

java.lang.Object

picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier

All Implemented Interfaces:

ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>

Enclosing class:

ReadBaseStratification

public static class ReadBaseStratification.LongShortHomopolymerStratifier
extends java.lang.Object
implements ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>

Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not). Read direction and only the preceding bases are taken into account.

Method Summary

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

Methods inherited from class java.lang.Object

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

Method Detail

stratify

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

Specified by:

stratify in interface ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>

getSuffix

public java.lang.String getSuffix()

Specified by:

getSuffix in interface ReadBaseStratification.RecordAndOffsetStratifier<ReadBaseStratification.LongShortHomopolymer>