Class TestCasesIntegrationEff


  • public class TestCasesIntegrationEff
    extends TestCasesIntegrationBase
    Test cases for other 'effect' issues
    Author:
    pcingola
    • Constructor Detail

      • TestCasesIntegrationEff

        public TestCasesIntegrationEff()
    • Method Detail

      • test_01

        @Test
        public void test_01()
        Test output order
      • test_01_canonical

        @Test
        public void test_01_canonical()
        Test output order: Canonical first
      • test_02

        @Test
        public void test_02()
        Test GATK option: At most one effect per VCF entry
      • test_03_EmptyVcf

        @Test
        public void test_03_EmptyVcf()
        Make sure that empty VCF does not trigger an exception when creating the summary
      • test_04

        @Test
        public void test_04()
        Test that CSV summary does not throw any error
      • test_05

        @Test
        public void test_05()
        GATK mode should not have SPLICE_REGION (it is currently not supported)
      • test_06

        @Test
        public void test_06()
        Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
      • test_07

        @Test
        public void test_07()
        Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
      • test_08_gatk_missing_annotations

        @Test
        public void test_08_gatk_missing_annotations()
        Fixing bug: GATK does not annotate all VCF entries