Class TestCasesVariantRealignment


  • public class TestCasesVariantRealignment
    extends TestCasesBase
    Test cases for variant realignment
    • Constructor Detail

      • TestCasesVariantRealignment

        public TestCasesVariantRealignment()
    • Method Detail

      • test_01

        @Test
        public void test_01()
        Shift by one position
      • test_02

        @Test
        public void test_02()
        No shift
      • test_03

        @Test
        public void test_03()
        Shift by one position
      • test_04_Intron

        @Test
        public void test_04_Intron()
        Shift by one position in an intron
      • test_05_savant

        @Test
        public void test_05_savant()
        Test case from Savant's poster http://www.well.ox.ac.uk/savant (Marton Munz, Elise Ruark, Nazneen Rahman, Gerton Lunter)
      • test_05_savant_opposite

        @Test
        public void test_05_savant_opposite()
      • test_06_savant

        @Test
        public void test_06_savant()
        Same as test Savant's test case, but using variant and GenomicSequences
      • test_07_savant

        @Test
        public void test_07_savant()
        Another test case fmor Savant's poster
      • test_08_reallyLongRealign

        @Test
        public void test_08_reallyLongRealign()
        This test should trigger progressive realignment. I.e. requiring more bases to the right in order to make a good alignment.
      • test_09_reallyLongRealign

        @Test
        public void test_09_reallyLongRealign()
        This test should trigger (AND fail) to make a progressive realignment. I.e. requiring more bases to the right in order to make a good alignment, but there are no more bases available from GenomicSequences.