Class TestCasesDnaSequence

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

public class TestCasesDnaSequence extends TestCasesBase
  • Constructor Details

    • TestCasesDnaSequence

      public TestCasesDnaSequence()
  • Method Details

    • randDnaSeqGetBasesTest

      public void randDnaSeqGetBasesTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
      Create random sequences and store them in a DnaSequence. Compare getting a few random bases from the original and DnaSequence sequences.
    • randDnaSeqGetBaseTest

      public void randDnaSeqGetBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
      Create random sequences and store them in a DnaSequence. Compare getting a single random base from the original and DnaSequence sequences.
    • randDnaSeqTest

      public void randDnaSeqTest(int numTests, int lenMask, long seed)
      Create random sequences and compare to storing them in a DnaSequence
    • randReplaceBaseTest

      public void randReplaceBaseTest(int numTests, int numTestsPerSeq, int lenMask, long seed)
      Create random sequences and store them in a DnaSequence. Compare after replacing random bases from the original and DnaSequence sequences.
    • randTestQual

      public void randTestQual(int numTests, int lenMask, long seed)
      Create random sequences (and qualities) and compare to storing them in a DnaAndQuality
    • test_01_short

      @Test public void test_01_short()
    • test_01_short_getBase

      @Test public void test_01_short_getBase()
    • test_01_short_getBases

      @Test public void test_01_short_getBases()
    • test_01_short_replaceBase

      @Test public void test_01_short_replaceBase()
    • test_02_long

      @Test public void test_02_long()
    • test_02_long_getBase

      @Test public void test_02_long_getBase()
    • test_02_long_getBases

      @Test public void test_02_long_getBases()
    • test_02_long_replaceBase

      @Test public void test_02_long_replaceBase()
    • test_04_Pe

      @Test public void test_04_Pe()
    • test_05_fastqReader

      @Test public void test_05_fastqReader()
    • test_05_quality_short

      @Test public void test_05_quality_short()
    • test_06_quality_long

      @Test public void test_06_quality_long()