Package org.snpeff.vcf
Class VcfConsequence
- java.lang.Object
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- org.snpeff.vcf.VcfConsequence
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public class VcfConsequence extends java.lang.Object
An 'CSQ' entry in a vcf line ('Consequence' from ENSEMBL's VEP) Format: ##INFO=- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
VCF_INFO_CSQ_NAME
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Constructor Summary
Constructors Constructor Description VcfConsequence(VcfConsequenceHeader vcfConsequenceHeader, java.lang.String csqString)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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()
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Field Detail
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VCF_INFO_CSQ_NAME
public static final java.lang.String VCF_INFO_CSQ_NAME
- See Also:
- Constant Field Values
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Constructor Detail
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VcfConsequence
public VcfConsequence(VcfConsequenceHeader vcfConsequenceHeader, java.lang.String csqString)
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Method Detail
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parse
public static java.util.List<VcfConsequence> parse(VcfConsequenceHeader vcfConsequenceHeader, java.lang.String csqString)
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parse
public static java.util.List<VcfConsequence> parse(VcfConsequenceHeader vcfConsequenceHeader, VcfEntry ve)
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get
public java.lang.String get(java.lang.String fieldName)
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getConsequence
public java.lang.String getConsequence()
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getFeature
public java.lang.String getFeature()
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getHgvsDna
public java.lang.String getHgvsDna()
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getHgvsProt
public java.lang.String getHgvsProt()
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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