Package org.snpeff.snpEffect.testCases.integration

Class TestCasesIntegrationCancer

java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
public class TestCasesIntegrationCancer extends TestCasesIntegrationBase
Test cases for cancer effect (difference betwee somatic an germline tissue)
Author:
pcingola

  • Constructor Details

    • TestCasesIntegrationCancer

      public TestCasesIntegrationCancer()

  • Method Details

    • test_01

      @Test public void test_01()
      Test Somatic vs Germline

    • test_02

      @Test public void test_02()
      Test Somatic vs Germline (using TXT file)

    • test_03_cancer_concurrent_modification

      @Test public void test_03_cancer_concurrent_modification()
      Concurrent modification issue on cancer samples (Intron.apply problem)

    • test_04

      @Test public void test_04()
      Test Somatic vs Germline: Check HGVS notation "c."

    • test_05

      @Test public void test_05()
      Cancer mutation is reversion to the REF base

    • test_06

      @Test public void test_06()
      Cancer mutation is reversion to the REF base

    • test_06_phased

      @Test public void test_06_phased()
      Cancer mutation is reversion to the REF base (pahsed VCF genotypes)

    • test_07

      @Test public void test_07()
      Cancer mutation is reversion to the REF base

    • test_07_phase

      @Test public void test_07_phase()
      Cancer mutation is reversion to the REF base