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