Class CompareToVep


  • public class CompareToVep
    extends java.lang.Object
    Compare our results to ENSEML's Variant Effect predictor's output
    Author:
    pcingola
    • Constructor Detail

      • CompareToVep

        public CompareToVep​(java.lang.String genomeName,
                            boolean verbose)
      • CompareToVep

        public CompareToVep​(java.lang.String genomeName,
                            java.lang.String[] addArgs,
                            boolean verbose)
    • Method Detail

      • checkComapred

        public boolean checkComapred()
      • compareVep

        public void compareVep​(java.lang.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 java.lang.String toString()
        Overrides:
        toString in class java.lang.Object