Class TestCasesIntegrationVcfs
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVcfs
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public class TestCasesIntegrationVcfs extends TestCasesIntegrationBase
VCF annotations test cases- 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 TestCasesIntegrationVcfs()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static void
create1kgFile()
Creates a test filevoid
test_01_vcf_bed_filter()
void
test_02_Annotating_LOF_Spaces()
Annotating LOF / NMD using a geneName that contains spaces triggers an Exception (it shouldn't happen)void
test_03_do_not_annotate_non_variants()
Non-variant VCF entries should be skipped (i.e.-
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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create1kgFile
public static void create1kgFile()
Creates a test file
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test_01_vcf_bed_filter
@Test public void test_01_vcf_bed_filter()
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test_02_Annotating_LOF_Spaces
@Test public void test_02_Annotating_LOF_Spaces()
Annotating LOF / NMD using a geneName that contains spaces triggers an Exception (it shouldn't happen)
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test_03_do_not_annotate_non_variants
@Test public void test_03_do_not_annotate_non_variants()
Non-variant VCF entries should be skipped (i.e. no annotation should be added)
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