Class CompareEffects
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.CompareEffects
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public class CompareEffects extends java.lang.Object
Compare effects in tests cases- Author:
- pcingola
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Constructor Summary
Constructors Constructor Description CompareEffects(java.lang.String genomeName, long randSeed, boolean verbose)
CompareEffects(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Config
getConfig()
void
initSnpEffPredictor()
java.util.List<Variant>
parseSnpEffectFile(java.lang.String variantFile)
Parse a variant file and return a listvoid
setUseAaNoNum(boolean useAaNoNum)
void
snpEffect(java.lang.String snpEffFile, java.lang.String transcriptId, boolean useShort)
Read snps from a file and compare them to 'out' SnpEffect predictor.void
snpEffect(java.util.List<Variant> variantList, java.lang.String transcriptId, boolean useShort, boolean negate)
Calculate snp effect for a list of snpsvoid
snpEffectNegate(java.lang.String snpEffFile, java.lang.String transcriptId, boolean useShort)
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Constructor Detail
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CompareEffects
public CompareEffects(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose)
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CompareEffects
public CompareEffects(java.lang.String genomeName, long randSeed, boolean verbose)
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Method Detail
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getConfig
public Config getConfig()
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initSnpEffPredictor
public void initSnpEffPredictor()
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parseSnpEffectFile
public java.util.List<Variant> parseSnpEffectFile(java.lang.String variantFile)
Parse a variant file and return a list
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setUseAaNoNum
public void setUseAaNoNum(boolean useAaNoNum)
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snpEffect
public void snpEffect(java.util.List<Variant> variantList, java.lang.String transcriptId, boolean useShort, boolean negate)
Calculate snp effect for a list of snps
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snpEffect
public void snpEffect(java.lang.String snpEffFile, java.lang.String transcriptId, boolean useShort)
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
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snpEffectNegate
public void snpEffectNegate(java.lang.String snpEffFile, java.lang.String transcriptId, boolean useShort)
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