Package org.snpeff.vcf

Class VcfConsequence

java.lang.Object

org.snpeff.vcf.VcfConsequence

public class VcfConsequence
extends java.lang.Object

An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP) Format: ##INFO=

Author:

pablocingolani

Field Summary

Fields

Modifier and Type	Field	Description
static java.lang.String	VCF_INFO_CSQ_NAME

Constructor Summary

Constructors

Constructor	Description
VcfConsequence(VcfConsequenceHeader vcfConsequenceHeader, java.lang.String csqString)

Method Summary

Modifier and Type	Method	Description
java.lang.String	get(java.lang.String fieldName)
java.lang.String	getConsequence()
java.lang.String	getFeature()
java.lang.String	getHgvsDna()
java.lang.String	getHgvsProt()
static java.util.List<VcfConsequence>	parse(VcfConsequenceHeader vcfConsequenceHeader, java.lang.String csqString)
static java.util.List<VcfConsequence>	parse(VcfConsequenceHeader vcfConsequenceHeader, VcfEntry ve)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

VCF_INFO_CSQ_NAME

public static final java.lang.String VCF_INFO_CSQ_NAME

See Also:

Constant Field Values

Constructor Detail

VcfConsequence

public VcfConsequence(VcfConsequenceHeader vcfConsequenceHeader,
                      java.lang.String csqString)

Method Detail

parse

public static java.util.List<VcfConsequence> parse(VcfConsequenceHeader vcfConsequenceHeader,
                                                   java.lang.String csqString)

parse

public static java.util.List<VcfConsequence> parse(VcfConsequenceHeader vcfConsequenceHeader,
                                                   VcfEntry ve)

get

public java.lang.String get(java.lang.String fieldName)

getConsequence

public java.lang.String getConsequence()

getFeature

public java.lang.String getFeature()

getHgvsDna

public java.lang.String getHgvsDna()

getHgvsProt

public java.lang.String getHgvsProt()

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object