htsjdk.samtools.util

Interface Locatable

All Known Subinterfaces:

BEDFeature, Feature

All Known Implementing Classes:

BAMRecord, FullBEDFeature, GeliTextFeature, Interval, SAMRecord, SimpleBEDFeature, SimpleFeature, VariantContext

public interface Locatable

Any class that has a single logical mapping onto the genome should implement Locatable positions should be reported as 1-based and closed at both ends

Method Summary

Methods

Modifier and Type	Method and Description
java.lang.String	getContig() Gets the contig name for the contig this is mapped to.
int	getEnd()
int	getStart()

Method Detail

getContig

java.lang.String getContig()

Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.

Returns:

name of the contig this is mapped to, potentially null

getStart

int getStart()

Returns:

1-based start position, undefined if getContig() == null

getEnd

int getEnd()

Returns:

1-based closed-ended position, undefined if getContig() == null