org.utgenome.util.sv
Class GeneticVariation

java.lang.Object
  org.utgenome.util.sv.GeneticVariation

Direct Known Subclasses:

EnhancedGeneticVariation

public class GeneticVariation
extends Object

genetic variation location [start, end), chr and allele (genotype) information

Author:

leo

Nested Class Summary

static class

GeneticVariation.VariationType

Field Summary

String	chr
int	indelLength
String	refBase
int	start
GeneticVariation.VariationType	variationType

Constructor Summary

GeneticVariation()

GeneticVariation(GeneticVariation other)

GeneticVariation(String chr, int start, String genotype)

Method Summary

IUPAC	getAltBase()
String	getGenotype()
void	setGenotype(String genotype)
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

variationType

public GeneticVariation.VariationType variationType

chr

public String chr

start

public int start

refBase

public String refBase

indelLength

public int indelLength

Constructor Detail

GeneticVariation

public GeneticVariation()

GeneticVariation

public GeneticVariation(String chr,
                        int start,
                        String genotype)

Parameters:

type -

chr -

start - 1-origin (inclusive)

end - 1-origin (exclusive)

genotype - A, C, AC, ACGT (genotype), *, +A (insertion to reference), -aatT (deletion from reference), etc.

GeneticVariation

public GeneticVariation(GeneticVariation other)

Method Detail

getAltBase

public IUPAC getAltBase()

getGenotype

public String getGenotype()

setGenotype

public void setGenotype(String genotype)

toString

public String toString()

Overrides:

toString in class Object