Class TestCasesHgvsBase

    • Field Detail

      • debug

        protected boolean debug
      • verbose

        protected boolean verbose
      • rand

        protected java.util.Random rand
      • config

        protected Config config
      • genome

        protected Genome genome
      • gene

        protected Gene gene
      • chromoSequence

        protected java.lang.String chromoSequence
      • chromoBases

        protected char[] chromoBases
    • Constructor Detail

      • TestCasesHgvsBase

        public TestCasesHgvsBase()
    • Method Detail

      • exonBase

        protected int exonBase​(char[] bases,
                               int pos,
                               int direction)
        Count how many bases are there until the exon
      • init

        protected void init()
      • initRand

        protected void initRand()
      • initSnpEffPredictor

        protected void initSnpEffPredictor​(boolean addUtrs,
                                           boolean onlyPlusStrand)
        Create a predictor
      • intronHgsv

        protected java.lang.String intronHgsv​(char[] bases,
                                              int j,
                                              int pos,
                                              java.lang.String refStr,
                                              java.lang.String altStr)
        Intronic HGS notation
      • snpEffect

        public void snpEffect​(java.lang.String genomeVer,
                              java.lang.String vcfFile)
        Run SnpEff on VCF file