Class TestCasesVariantRealignment

java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesVariantRealignment

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

    • TestCasesVariantRealignment

      public TestCasesVariantRealignment()
  • Method Details

    • init

      protected void init()
      Overrides:
      init in class TestCasesBase
    • 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.