Class CompareEffects
java.lang.Object
org.snpeff.snpEffect.testCases.integration.CompareEffects
Compare effects in tests cases
- Author:
- pcingola
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Constructor Summary
ConstructorsConstructorDescriptionCompareEffects
(String genomeName, long randSeed, boolean verbose) CompareEffects
(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose) -
Method Summary
Modifier and TypeMethodDescriptionvoid
parseSnpEffectFile
(String variantFile) Parse a variant file and return a listvoid
setUseAaNoNum
(boolean useAaNoNum) void
Read snps from a file and compare them to 'out' SnpEffect predictor.void
Calculate snp effect for a list of snpsvoid
snpEffectNegate
(String snpEffFile, String transcriptId, boolean useShort)
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Constructor Details
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CompareEffects
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CompareEffects
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Method Details
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getConfig
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initSnpEffPredictor
public void initSnpEffPredictor() -
parseSnpEffectFile
Parse a variant file and return a list -
setUseAaNoNum
public void setUseAaNoNum(boolean useAaNoNum) -
snpEffect
public void snpEffect(List<Variant> variantList, String transcriptId, boolean useShort, boolean negate) Calculate snp effect for a list of snps -
snpEffect
Read snps from a file and compare them to 'out' SnpEffect predictor. Make sure at least one effect matched the 'id' in the input TXT file -
snpEffectNegate
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