Class TestCasesHgvsBase

java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesHgvsBase
Direct Known Subclasses:
TestCasesHgvsExon, TestCasesHgvsIntron

public class TestCasesHgvsBase extends Object
Test random SNP changes
Author:
pcingola
  • Field Details

    • debug

      protected boolean debug
    • verbose

      protected boolean verbose
    • rand

      protected Random rand
    • config

      protected Config config
    • genome

      protected Genome genome
    • chromosome

      protected Chromosome chromosome
    • gene

      protected Gene gene
    • transcript

      protected Transcript transcript
    • snpEffectPredictor

      protected SnpEffectPredictor snpEffectPredictor
    • chromoSequence

      protected String chromoSequence
    • chromoBases

      protected char[] chromoBases
  • Constructor Details

    • TestCasesHgvsBase

      public TestCasesHgvsBase()
  • Method Details

    • 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 String intronHgsv(char[] bases, int j, int pos, String refStr, String altStr)
      Intronic HGS notation
    • snpEffect

      public void snpEffect(String genomeVer, String vcfFile)
      Run SnpEff on VCF file