Class TestCasesHgvsBase
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
- Direct Known Subclasses:
TestCasesHgvsExon
,TestCasesHgvsIntron
Test random SNP changes
- Author:
- pcingola
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Field Summary
FieldsModifier and TypeFieldDescriptionprotected char[]
protected String
protected Chromosome
protected Config
protected boolean
protected Gene
protected Genome
protected Random
protected SnpEffectPredictor
protected Transcript
protected boolean
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected int
exonBase
(char[] bases, int pos, int direction) Count how many bases are there until the exonprotected void
init()
protected void
initRand()
protected void
initSnpEffPredictor
(boolean addUtrs, boolean onlyPlusStrand) Create a predictorprotected String
intronHgsv
(char[] bases, int j, int pos, String refStr, String altStr) Intronic HGS notationvoid
Run SnpEff on VCF file
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Field Details
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debug
protected boolean debug -
verbose
protected boolean verbose -
rand
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config
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genome
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chromosome
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gene
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transcript
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snpEffectPredictor
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chromoSequence
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chromoBases
protected char[] chromoBases
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Constructor Details
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TestCasesHgvsBase
public TestCasesHgvsBase()
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Method Details
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exonBase
protected int exonBase(char[] bases, int pos, int direction) Count how many bases are there until the exon -
init
protected void init() -
initRand
protected void initRand() -
initSnpEffPredictor
protected void initSnpEffPredictor(boolean addUtrs, boolean onlyPlusStrand) Create a predictor -
intronHgsv
Intronic HGS notation -
snpEffect
Run SnpEff on VCF file
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