Class 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.