Class TestCasesEffectCollapse
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesEffectCollapse
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public class TestCasesEffectCollapse extends TestCasesBase
Test Splice sites variantsThe sample transcript used is: Transcript:1:751-1139, strand: +, id:transcript_0, Protein Exons: 1:751-810 'exon_0_0', rank: 1, frame: ., sequence: cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgca 1:1013-1139 'exon_0_1', rank: 2, frame: ., sequence: cttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa CDS : cgattgacctacatagtaatgagttttgttggtccgtaagacttcgcccaaaaccgcgcacttcgactactcgggggtctaagcacgttttctgcagggaaagtaatatatgcttgtgcgcaaccatggtaacagggattcacggccccgttaatggtatgacctaagccccatacgagtcatccaa Protein : RLTYIVMSFVGP*DFAQNRALRLLGGLSTFSAGKVIYACAQPW*QGFTAPLMV*PKPHTSHP?
- Author:
- pcingola
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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 TestCasesEffectCollapse()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
init()
void
test_01()
void
test_02()
void
test_03()
void
test_04()
void
test_05()
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Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
after, before, checkApply, checkApplyDel, checkApplyIns, checkApplyMixed, checkApplyMnp, checkApplySnp, checkEffect, checkEffect, formatVersion, hasEffect, initRand, initSnpEffPredictor, initSnpEffPredictor, path, pathClassName, prependSequenceToFirstExon
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Method Detail
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init
protected void init()
- Overrides:
init
in classTestCasesBase
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test_01
@Test public void test_01()
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test_02
@Test public void test_02()
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test_03
@Test public void test_03()
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test_04
@Test public void test_04()
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test_05
@Test public void test_05()
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