Package org.snpeff.snpEffect.testCases.integration

Class CompareEffects

  • public class CompareEffects
extends java.lang.Object
    Compare effects in tests cases
    Author:
    pcingola

    • Constructor Summary

      Constructors 
      Constructor Description
      CompareEffects​(java.lang.String genomeName, long randSeed, boolean verbose)  
      CompareEffects​(SnpEffectPredictor snpEffectPredictor, long randSeed, boolean verbose)  

    • 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 list
      void 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 snps
      void snpEffectNegate​(java.lang.String snpEffFile, java.lang.String transcriptId, boolean useShort)  

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • CompareEffects

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

      • CompareEffects

        public CompareEffects​(java.lang.String genomeName,
                      long randSeed,
                      boolean verbose)

    • Method Detail

      • getConfig

        public Config getConfig()

      • initSnpEffPredictor

        public void initSnpEffPredictor()

      • parseSnpEffectFile

        public java.util.List<Variant> parseSnpEffectFile​(java.lang.String variantFile)
        Parse a variant file and return a list

      • setUseAaNoNum

        public void setUseAaNoNum​(boolean useAaNoNum)

      • 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

      • 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

      • snpEffectNegate

        public void snpEffectNegate​(java.lang.String snpEffFile,
                            java.lang.String transcriptId,
                            boolean useShort)