Class TestCasesIntegrationCancer
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationCancer
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public class TestCasesIntegrationCancer extends TestCasesIntegrationBase
Test cases for cancer effect (difference betwee somatic an germline tissue)- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
BASE_DIR, debug, ignoreErrors, prefixes, shiftHgvs, SHOW_EVERY, testsDir, testType, verbose
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Constructor Summary
Constructors Constructor Description TestCasesIntegrationCancer()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01()
Test Somatic vs Germlinevoid
test_02()
Test Somatic vs Germline (using TXT file)void
test_03_cancer_concurrent_modification()
Concurrent modification issue on cancer samples (Intron.apply problem)void
test_04()
Test Somatic vs Germline: Check HGVS notation "c."void
test_05()
Cancer mutation is reversion to the REF basevoid
test_06()
Cancer mutation is reversion to the REF basevoid
test_06_phased()
Cancer mutation is reversion to the REF base (pahsed VCF genotypes)void
test_07()
Cancer mutation is reversion to the REF basevoid
test_07_phase()
Cancer mutation is reversion to the REF base-
Methods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
applyTranscript, before, build, buildAndCompare, buildEmbl, buildGeneBank, buildGeneBank, buildGetBuildCmd, buildGff3AndCompare, buildGtfAndCompare, checkHgvs, checkNoChange, checkTranscriptError, compareHgvs, compareHgvs, compareVep, compareVepSO, init, loadSnpEffectPredictor, path, pathClassName, pathMigrate, showTranscripts, showTranscripts, snpEffect, snpEffect, snpEffectCancer
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Method Detail
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test_01
@Test public void test_01()
Test Somatic vs Germline
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test_02
@Test public void test_02()
Test Somatic vs Germline (using TXT file)
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test_03_cancer_concurrent_modification
@Test public void test_03_cancer_concurrent_modification()
Concurrent modification issue on cancer samples (Intron.apply problem)
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test_04
@Test public void test_04()
Test Somatic vs Germline: Check HGVS notation "c."
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test_05
@Test public void test_05()
Cancer mutation is reversion to the REF base
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test_06
@Test public void test_06()
Cancer mutation is reversion to the REF base
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test_06_phased
@Test public void test_06_phased()
Cancer mutation is reversion to the REF base (pahsed VCF genotypes)
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test_07
@Test public void test_07()
Cancer mutation is reversion to the REF base
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test_07_phase
@Test public void test_07_phase()
Cancer mutation is reversion to the REF base
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