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)