Package org.snpeff.snpEffect.testCases.integration

Class CompareEffects

java.lang.Object
org.snpeff.snpEffect.testCases.integration.CompareEffects
public class CompareEffects extends Object
Compare effects in tests cases
Author:
pcingola

  • Constructor Details

    • CompareEffects

      public CompareEffects(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose)

    • CompareEffects

      public CompareEffects(String genomeName, long randSeed, boolean verbose)

  • Method Details

    • getConfig

      public Config getConfig()

    • initSnpEffPredictor

      public void initSnpEffPredictor()

    • parseSnpEffectFile

      public List<Variant> parseSnpEffectFile(String variantFile)
      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

      public void snpEffect(String snpEffFile, 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

    • snpEffectNegate

      public void snpEffectNegate(String snpEffFile, String transcriptId, boolean useShort)