Package org.snpeff.snpEffect
Class Hgvs
- java.lang.Object
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- org.snpeff.snpEffect.Hgvs
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- Direct Known Subclasses:
HgvsDna
,HgvsProtein
public class Hgvs extends java.lang.Object
HGSV notation References: http://www.hgvs.org/- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description protected boolean
duplication
protected Genome
genome
protected boolean
hgvsTrId
protected Marker
marker
static int
MAX_SEQUENCE_LEN_HGVS
protected boolean
strandMinus
protected boolean
strandPlus
protected Transcript
tr
protected Variant
variant
protected VariantEffect
variantEffect
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Constructor Summary
Constructors Constructor Description Hgvs(VariantEffect variantEffect)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
initStrand()
static java.lang.String
parseTranscript(java.lang.String hgvs)
static java.lang.String
removeTranscript(java.lang.String hgvs)
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Field Detail
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MAX_SEQUENCE_LEN_HGVS
public static final int MAX_SEQUENCE_LEN_HGVS
- See Also:
- Constant Field Values
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variantEffect
protected VariantEffect variantEffect
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variant
protected Variant variant
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marker
protected Marker marker
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tr
protected Transcript tr
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genome
protected Genome genome
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duplication
protected boolean duplication
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strandPlus
protected boolean strandPlus
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strandMinus
protected boolean strandMinus
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hgvsTrId
protected boolean hgvsTrId
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Constructor Detail
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Hgvs
public Hgvs(VariantEffect variantEffect)
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