Class TestCasesIntegrationVariant


  • public class TestCasesIntegrationVariant
    extends java.lang.Object
    Test cases for variants
    Author:
    pcingola
    • Constructor Detail

      • TestCasesIntegrationVariant

        public TestCasesIntegrationVariant()
    • Method Detail

      • test_08

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

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

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

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

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

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

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

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

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

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

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

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

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

        public void test_25_exon_bases()
      • test_26_chr15_78909452

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

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

        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

        public void test_30_RareAa()
        Rare Amino acid
      • test_31_CodonTable

        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

        public void test_32_StartGained()
        Start gained
      • test_33_StartGained_NOT

        public void test_33_StartGained_NOT()
        Not start gained
      • test_34_StartGained

        public void test_34_StartGained()
        Start gained
      • test_35_StartGained_NOT

        public void test_35_StartGained_NOT()
        Not start gained
      • test_36_EffectImpact

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

        public void test_38_NON_SYNONYMOUS_START()
        Test