Package org.snpeff.snpEffect.testCases.integration

Class TestCasesIntegrationMixedVariants

java.lang.Object

org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase

org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMixedVariants

public class TestCasesIntegrationMixedVariants
extends TestCasesIntegrationBase

Test mixed variants

Author:

pcingola

Field Summary

Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase

BASE_DIR, debug, ignoreErrors, prefixes, shiftHgvs, SHOW_EVERY, testsDir, testType, verbose

Constructor Summary

Constructors

Constructor	Description
TestCasesIntegrationMixedVariants()

Method Summary

Modifier and Type	Method	Description
void	compareVep(java.lang.String genome, java.lang.String vcf)	Compare with results from ENSEMBL's VEP to SnpEff Use VCF having VEP's results
void	test_01_MixedVep()	Make sure we can read VCF and parse variants without producing any exception
void	test_02_MixedVep()
void	test_03_MixedVep()
void	test_04_MixedVep()
void	test_05_MixedVep()
void	test_06_MixedVep()
void	test_07_MixedVep()
void	test_08_MixedVep()
void	test_09_MixedVep()
void	test_11_ExonRank()

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TestCasesIntegrationMixedVariants

public TestCasesIntegrationMixedVariants()

Method Detail

compareVep

public void compareVep(java.lang.String genome,
                       java.lang.String vcf)

Compare with results from ENSEMBL's VEP to SnpEff Use VCF having VEP's results

test_01_MixedVep

@Test
public void test_01_MixedVep()

Make sure we can read VCF and parse variants without producing any exception

test_02_MixedVep

@Test
public void test_02_MixedVep()

test_03_MixedVep

@Test
public void test_03_MixedVep()

test_04_MixedVep

@Test
public void test_04_MixedVep()

test_05_MixedVep

@Test
public void test_05_MixedVep()

test_06_MixedVep

@Test
public void test_06_MixedVep()

test_07_MixedVep

@Test
public void test_07_MixedVep()

test_08_MixedVep

@Test
public void test_08_MixedVep()

test_09_MixedVep

@Test
public void test_09_MixedVep()

test_11_ExonRank

@Test
public void test_11_ExonRank()