Class TestCasesIntegrationHgvsUpDownStream
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationHgvsUpDownStream
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public class TestCasesIntegrationHgvsUpDownStream extends TestCasesIntegrationBase
Test cases for HGVS notation
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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 TestCasesIntegrationHgvsUpDownStream()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01_hgvs_upstream()
Test for HGVS.C notation on upstream variantsvoid
test_02_hgvs_downstream()
Test for HGVS.C notation on downstream variantsvoid
test_03_hgvs_upstream_del()
Test that CSV summary does not throw any errorvoid
test_04_hgvs_upstream_negative_strand()
Test HGVS.C upstream of a variant affecting a transcript on the negative strandvoid
test_05_hgvs_downstream_negative_strand()
Test HGVS.C upstream of a variant affecting a transcript on the negative strand-
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_hgvs_upstream
public void test_01_hgvs_upstream()
Test for HGVS.C notation on upstream variants
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test_02_hgvs_downstream
public void test_02_hgvs_downstream()
Test for HGVS.C notation on downstream variants
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test_03_hgvs_upstream_del
public void test_03_hgvs_upstream_del()
Test that CSV summary does not throw any error
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test_04_hgvs_upstream_negative_strand
public void test_04_hgvs_upstream_negative_strand()
Test HGVS.C upstream of a variant affecting a transcript on the negative strand
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test_05_hgvs_downstream_negative_strand
public void test_05_hgvs_downstream_negative_strand()
Test HGVS.C upstream of a variant affecting a transcript on the negative strand
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