Class TestCasesAnnParse
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesAnnParse
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public class TestCasesAnnParse extends TestCasesBase
Test case for parsing ANN fields
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, BASE_DIR, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, prefixes, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, testType, transcript, verbose
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Constructor Summary
Constructors Constructor Description TestCasesAnnParse()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_EffectType()
Make sure all effect_tpyes have appropriate impacts, regions, etc.void
test_old_SO()
void
test_old_SO_vcf()
void
testCase_tfbs_ablation()
Make sure there are no exceptions thrown when parsing TFBS_abalation SO term-
Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, init, initRand, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
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Method Detail
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test_EffectType
@Test public void test_EffectType()
Make sure all effect_tpyes have appropriate impacts, regions, etc.
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test_old_SO
@Test public void test_old_SO()
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test_old_SO_vcf
@Test public void test_old_SO_vcf()
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testCase_tfbs_ablation
@Test public void testCase_tfbs_ablation()
Make sure there are no exceptions thrown when parsing TFBS_abalation SO term
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