Package org.snpeff.snpEffect.testCases.integration

Class CompareToVep

java.lang.Object
org.snpeff.snpEffect.testCases.integration.CompareToVep
public class CompareToVep extends Object
Compare our results to ENSEML's Variant Effect predictor's output
Author:
pcingola

  • Constructor Details

    • CompareToVep

      public CompareToVep(String genomeName, boolean verbose)

    • CompareToVep

      public CompareToVep(String genomeName, String[] addArgs, boolean verbose)

  • Method Details

    • checkComapred

      public boolean checkComapred()

    • compareVep

      public void compareVep(String vcf)
      Compare all VCF entries

    • setCompareHgvs

      public void setCompareHgvs()

    • setCompareHgvsDna

      public void setCompareHgvsDna(boolean compareHgvsDna)

    • setCompareHgvsProt

      public void setCompareHgvsProt(boolean compareHgvsProt)

    • setOnlyProtein

      public void setOnlyProtein(boolean onlyProtein)

    • setShiftHgvs

      public void setShiftHgvs(boolean shiftHgvs)

    • setStrict

      public void setStrict(boolean strict)

    • toString

      public String toString()
      Overrides:
      toString in class Object