Package org.snpeff.snpEffect
Class Hgvs
java.lang.Object
org.snpeff.snpEffect.Hgvs
- Direct Known Subclasses:
HgvsDna
,HgvsProtein
HGSV notation
References: http://www.hgvs.org/
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected boolean
protected Genome
protected boolean
protected Marker
static final int
protected boolean
protected boolean
protected Transcript
protected Variant
protected VariantEffect
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
static String
parseTranscript
(String hgvs) static String
removeTranscript
(String hgvs)
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Field Details
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MAX_SEQUENCE_LEN_HGVS
public static final int MAX_SEQUENCE_LEN_HGVS- See Also:
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variantEffect
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variant
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marker
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tr
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genome
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duplication
protected boolean duplication -
strandPlus
protected boolean strandPlus -
strandMinus
protected boolean strandMinus -
hgvsTrId
protected boolean hgvsTrId
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Constructor Details
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Hgvs
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Method Details
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parseTranscript
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removeTranscript
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initStrand
protected void initStrand()
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