htsjdk.tribble.gelitext

Class GeliTextFeature

java.lang.Object

htsjdk.tribble.gelitext.GeliTextFeature

All Implemented Interfaces:

Locatable, Feature

Deprecated.

this is deprecated and no longer supported

@Deprecated
public class GeliTextFeature
extends java.lang.Object
implements Feature

Class GeliTextFeature

This is a feature for the Geli text object, which is the text version of the Geli binary genotyping format.

Constructor Summary

Constructors

Constructor and Description
GeliTextFeature(java.lang.String contig, long position, char refBase, int depthOfCoverage, int maximumMappingQual, DiploidGenotype genotype, double LODBestToReference, double LODBestToNext, double[] likelihoods) Deprecated. Create a geli text feature, given:

Method Summary

Methods

Modifier and Type	Method and Description
boolean	equals(java.lang.Object o) Deprecated.
java.lang.String	getChr() Deprecated.
java.lang.String	getContig() Deprecated. Gets the contig name for the contig this is mapped to.
int	getDepthOfCoverage() Deprecated.
int	getEnd() Deprecated. Return the end position following 1-based fully closed conventions.
DiploidGenotype	getGenotype() Deprecated.
double[]	getLikelihoods() Deprecated.
double	getLODBestToNext() Deprecated.
double	getLODBestToReference() Deprecated.
int	getMaximumMappingQual() Deprecated.
char	getRefBase() Deprecated.
int	getStart() Deprecated. Return the start position in 1-based coordinates (first base is 1)

Methods inherited from class java.lang.Object

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

Constructor Detail

GeliTextFeature

public GeliTextFeature(java.lang.String contig,
               long position,
               char refBase,
               int depthOfCoverage,
               int maximumMappingQual,
               DiploidGenotype genotype,
               double LODBestToReference,
               double LODBestToNext,
               double[] likelihoods)

Deprecated.

Create a geli text feature, given:

Parameters:

contig - the contig

position - the position on the contig

refBase - the reference base

depthOfCoverage - the depth of coverage at this position

maximumMappingQual - the maximum mapping quality of a read at this position

genotype - the called genotype

LODBestToReference - the LOD score of the best to the reference

LODBestToNext - the LOD score of the best to the next best genotype

likelihoods - the array of all genotype likelihoods, in ordinal ordering

Method Detail

getChr

@Deprecated
public java.lang.String getChr()

Deprecated.

Return the features reference sequence name, e.g chromosome or contig

Specified by:

getChr in interface Feature

getContig

public java.lang.String getContig()

Deprecated.

Description copied from interface: Locatable

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

Specified by:

getContig in interface Locatable

Returns:

name of the contig this is mapped to, potentially null

getStart

public int getStart()

Deprecated.

Return the start position in 1-based coordinates (first base is 1)

Specified by:

getStart in interface Locatable

Returns:

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

getEnd

public int getEnd()

Deprecated.

Return the end position following 1-based fully closed conventions. The length of a feature is end - start + 1;

Specified by:

getEnd in interface Locatable

Returns:

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

getRefBase

public char getRefBase()

Deprecated.

getDepthOfCoverage

public int getDepthOfCoverage()

Deprecated.

getMaximumMappingQual

public int getMaximumMappingQual()

Deprecated.

getGenotype

public DiploidGenotype getGenotype()

Deprecated.

getLODBestToNext

public double getLODBestToNext()

Deprecated.

getLODBestToReference

public double getLODBestToReference()

Deprecated.

getLikelihoods

public double[] getLikelihoods()

Deprecated.

equals

public boolean equals(java.lang.Object o)

Deprecated.

Overrides:

equals in class java.lang.Object