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
All Methods Instance Methods Concrete Methods 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 resultsvoid
test_01_MixedVep()
Make sure we can read VCF and parse variants without producing any exceptionvoid
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
-
-
-
-
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()
-
-