Class TestCasesIntegrationGff3
- java.lang.Object
-
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
-
- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationGff3
-
public class TestCasesIntegrationGff3 extends TestCasesIntegrationBase
Test case for GFF3 file parsing- Author:
- pcingola
-
-
Field Summary
-
Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
debug, ignoreErrors, shiftHgvs, SHOW_EVERY, testsDir, verbose
-
-
Constructor Summary
Constructors Constructor Description TestCasesIntegrationGff3()
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
after()
void
before()
void
testCase_01_Exon_Simple()
void
testCase_02_ExonIn()
void
testCase_03_ExonOut()
void
testCase_04_AthalianaTair10_AT5G66790()
void
testCase_05_PaeruPA14muccA()
void
testCase_06_Ppersica()
void
testCase_07_Rice5()
void
testCase_08_Vibrio()
void
testCase_09()
void
testCase_09_AP()
void
testCase_10_MaizeZmB73()
Exon.frameCorrection: Exon too short (size: 1), cannot correct frame!void
testCase_11_mita()
Test for bug: Infinite loop when looking up "Parent ID" in some GFF3 files-
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
-
-
-
-
Method Detail
-
after
public void after()
-
before
public void before()
-
testCase_01_Exon_Simple
public void testCase_01_Exon_Simple()
-
testCase_02_ExonIn
public void testCase_02_ExonIn()
-
testCase_03_ExonOut
public void testCase_03_ExonOut()
-
testCase_04_AthalianaTair10_AT5G66790
public void testCase_04_AthalianaTair10_AT5G66790()
-
testCase_05_PaeruPA14muccA
public void testCase_05_PaeruPA14muccA()
-
testCase_06_Ppersica
public void testCase_06_Ppersica()
-
testCase_07_Rice5
public void testCase_07_Rice5()
-
testCase_08_Vibrio
public void testCase_08_Vibrio()
-
testCase_09
public void testCase_09()
-
testCase_09_AP
public void testCase_09_AP()
-
testCase_10_MaizeZmB73
public void testCase_10_MaizeZmB73()
Exon.frameCorrection: Exon too short (size: 1), cannot correct frame!
-
testCase_11_mita
public void testCase_11_mita()
Test for bug: Infinite loop when looking up "Parent ID" in some GFF3 files
-
-