Class TestCasesIntegrationEff
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
Test cases for other 'effect' issues
- Author:
- pcingola
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Field Summary
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
test_01()
Test output ordervoid
Test output order: Canonical firstvoid
test_02()
Test GATK option: At most one effect per VCF entryvoid
Make sure that empty VCF does not trigger an exception when creating the summaryvoid
test_04()
Test that CSV summary does not throw any errorvoid
test_05()
GATK mode should not have SPLICE_REGION (it is currently not supported)void
test_06()
Test an MNP at the end of the transcript: We should be able to annotate without throwing any errorvoid
test_07()
Test an MNP at the end of the transcript: We should be able to annotate without throwing any errorvoid
Fixing bug: GATK does not annotate all VCF entriesMethods 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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Constructor Details
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TestCasesIntegrationEff
public TestCasesIntegrationEff()
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Method Details
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test_01
@Test public void test_01()Test output order -
test_01_canonical
@Test public void test_01_canonical()Test output order: Canonical first -
test_02
@Test public void test_02()Test GATK option: At most one effect per VCF entry -
test_03_EmptyVcf
@Test public void test_03_EmptyVcf()Make sure that empty VCF does not trigger an exception when creating the summary -
test_04
@Test public void test_04()Test that CSV summary does not throw any error -
test_05
@Test public void test_05()GATK mode should not have SPLICE_REGION (it is currently not supported) -
test_06
@Test public void test_06()Test an MNP at the end of the transcript: We should be able to annotate without throwing any error -
test_07
@Test public void test_07()Test an MNP at the end of the transcript: We should be able to annotate without throwing any error -
test_08_gatk_missing_annotations
@Test public void test_08_gatk_missing_annotations()Fixing bug: GATK does not annotate all VCF entries
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