Class TestCasesIntegrationGff3
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
Test case for GFF3 file parsing
- 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
Methods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
applyTranscript, 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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TestCasesIntegrationGff3
public TestCasesIntegrationGff3()
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Method Details
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after
@AfterEach public void after() -
before
@BeforeEach public void before()- Overrides:
before
in classTestCasesIntegrationBase
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testCase_01_Exon_Simple
@Test public void testCase_01_Exon_Simple() -
testCase_02_ExonIn
@Test public void testCase_02_ExonIn() -
testCase_03_ExonOut
@Test public void testCase_03_ExonOut() -
testCase_04_AthalianaTair10_AT5G66790
@Test public void testCase_04_AthalianaTair10_AT5G66790() -
testCase_05_PaeruPA14muccA
@Test public void testCase_05_PaeruPA14muccA() -
testCase_06_Ppersica
@Test public void testCase_06_Ppersica() -
testCase_07_Rice5
@Test public void testCase_07_Rice5() -
testCase_08_Vibrio
@Test public void testCase_08_Vibrio() -
testCase_09
@Test public void testCase_09() -
testCase_09_AP
@Test public void testCase_09_AP() -
testCase_10_MaizeZmB73
@Test public void testCase_10_MaizeZmB73()Exon.frameCorrection: Exon too short (size: 1), cannot correct frame! -
testCase_11_mita
@Test public void testCase_11_mita()Test for bug: Infinite loop when looking up "Parent ID" in some GFF3 files
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