Class TestCasesIntegrationEff
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationEff
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public class TestCasesIntegrationEff extends TestCasesIntegrationBase
Test cases for other 'effect' issues- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
debug, ignoreErrors, shiftHgvs, SHOW_EVERY, testsDir, verbose
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Constructor Summary
Constructors Constructor Description TestCasesIntegrationEff()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01()
Test output ordervoid
test_01_canonical()
Test output order: Canonical firstvoid
test_02()
Test GATK option: At most one effect per VCF entryvoid
test_03_EmptyVcf()
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
test_08_gatk_missing_annotations()
Fixing bug: GATK does not annotate all VCF entries-
Methods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
appyTranscript, build, buildAndCompare, buildEmbl, buildGeneBank, buildGff3AndCompare, buildGtfAndCompare, checkHgvs, checkNoChange, checkTranscriptError, compareHgvs, compareHgvs, compareVep, compareVepSO, init, loadSnpEffectPredictor, showTranscripts, showTranscripts, snpEffect, snpEffect, snpEffectCancer
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Method Detail
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test_01
public void test_01()
Test output order
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test_01_canonical
public void test_01_canonical()
Test output order: Canonical first
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test_02
public void test_02()
Test GATK option: At most one effect per VCF entry
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test_03_EmptyVcf
public void test_03_EmptyVcf()
Make sure that empty VCF does not trigger an exception when creating the summary
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test_04
public void test_04()
Test that CSV summary does not throw any error
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test_05
public void test_05()
GATK mode should not have SPLICE_REGION (it is currently not supported)
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test_06
public void test_06()
Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
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test_07
public void test_07()
Test an MNP at the end of the transcript: We should be able to annotate without throwing any error
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test_08_gatk_missing_annotations
public void test_08_gatk_missing_annotations()
Fixing bug: GATK does not annotate all VCF entries
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