Class TestCasesIntegrationVariant

java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant

public class TestCasesIntegrationVariant extends TestCasesIntegrationBase
Test cases for variants
Author:
pcingola
  • Constructor Details

    • TestCasesIntegrationVariant

      public TestCasesIntegrationVariant()
  • Method Details

    • test_08

      @Test public void test_08()
      CDS test (CDS = CoDing Sequences) Build CDS form exon sequences
    • test_09

      @Test public void test_09()
      Test SNP effect predictor for a transcript
    • test_11

      @Test public void test_11()
      Test SNP effect predictor: Test UTR distances, Up/Downstream distances
    • test_12

      @Test public void test_12()
      Test SNP effect predictor: Test Splice sites
    • test_12_2

      @Test public void test_12_2()
      Test SNP effect predictor: Test Splice sites (make sure they are only 2 bases long)
    • test_19

      @Test public void test_19()
      Test SNP effect predictor: Test start codon gained
    • test_20

      @Test public void test_20()
      Test SNP effect predictor: Test start codon gained (reverse strand)
    • test_21

      @Test public void test_21()
      Test SNP effect predictor for a transcript (Insertions)
    • test_21_2

      @Test public void test_21_2()
      Test SNP effect predictor for a transcript (Insertions)
    • test_21_3

      @Test public void test_21_3()
      Test SNP effect predictor for a transcript (Insertions)
    • test_22

      @Test public void test_22()
      Read file test: Should throw an exception (chromosome not found)
    • test_23_MNP_on_exon_edge

      @Test public void test_23_MNP_on_exon_edge()
      Test SNP effect predictor for a transcript (Insertions)
    • test_24_delete_exon_utr

      @Test public void test_24_delete_exon_utr()
      Test SNP effect predictor for a transcript (Insertions)
    • test_25_exon_bases

      @Test public void test_25_exon_bases()
    • test_26_chr15_78909452

      @Test public void test_26_chr15_78909452()
      Test SNP effect predictor for a transcript (Insertions)
    • test_28_Splice_mm37_ENSMUSG00000005763

      @Test public void test_28_Splice_mm37_ENSMUSG00000005763()
      Splice site: Bug reported by Wang, Xusheng
    • test_29_Intergenic_in_Gene

      @Test public void test_29_Intergenic_in_Gene()
      Test effect when hits a gene, but not any transcript within a gene. This is an extremely weird case, might be an annotation problem.
    • test_30_RareAa

      @Test public void test_30_RareAa()
      Rare Amino acid
    • test_31_CodonTable

      @Test public void test_31_CodonTable()
      MT chromo Effectusing an alternative codon table: Codon change : atA / atG Standard codon table : Ile / Met => NON_SYNONYMOUS Mithocondria codon table: Met / Met => SYNONYMOUS
    • test_32_StartGained

      @Test public void test_32_StartGained()
      Start gained
    • test_33_StartGained_NOT

      @Test public void test_33_StartGained_NOT()
      Not start gained
    • test_34_StartGained

      @Test public void test_34_StartGained()
      Start gained
    • test_35_StartGained_NOT

      @Test public void test_35_StartGained_NOT()
      Not start gained
    • test_36_EffectImpact

      @Test public void test_36_EffectImpact()
      Make sure all variant effects have appropriate impacts
    • test_38_NON_SYNONYMOUS_START

      @Test public void test_38_NON_SYNONYMOUS_START()
      Test