Class TestCasesApplyIns
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
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- org.snpeff.snpEffect.testCases.unity.TestCasesApplyIns
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public class TestCasesApplyIns extends TestCasesBaseApply
Test cases: apply a variant (INS) to a transcript
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBase
addUtrs, chromoBases, chromoSequence, chromosome, codonTable, config, debug, gene, genome, genomeName, maxExons, maxGeneLen, maxTranscripts, minExons, numGenes, onlyMinusStrand, onlyPlusStrand, rand, randSeed, shiftHgvs, snpEffectPredictor, spliceRegionExonSize, spliceRegionIntronMax, spliceRegionIntronMin, transcript, verbose
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Constructor Summary
Constructors Constructor Description TestCasesApplyIns()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_apply_variant_01()
Variant before exonvoid
test_apply_variant_02()
Variant before exonvoid
test_apply_variant_03()
Variant overlapping exon startvoid
test_apply_variant_04()
Variant at exon startvoid
test_apply_variant_05()
Variant in exonvoid
test_apply_variant_06()
Variant in exonvoid
test_apply_variant_07()
Variant overlapping exon endvoid
test_apply_variant_08()
Variant right after exon endvoid
test_apply_variant_09()
Variant after exon endvoid
test_apply_variant_10()
Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exonvoid
test_apply_variant_11()
Variant over exon: variant is larger than exon and starts right at exons start and ends after exon endvoid
test_apply_variant_12()
Variant over exon: variant is larger than exon, starts before exon start and end right at exon endvoid
test_apply_variant_13()
Variant over exon: variant is on the same coordiantes as exon-
Methods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
initSnpEffPredictor
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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, init, initRand, initSnpEffPredictor, prependSequenceToFirstExon, showTranscripts
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Method Detail
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test_apply_variant_01
public void test_apply_variant_01()
Variant before exon
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test_apply_variant_02
public void test_apply_variant_02()
Variant before exon
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test_apply_variant_03
public void test_apply_variant_03()
Variant overlapping exon start
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test_apply_variant_04
public void test_apply_variant_04()
Variant at exon start
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test_apply_variant_05
public void test_apply_variant_05()
Variant in exon
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test_apply_variant_06
public void test_apply_variant_06()
Variant in exon
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test_apply_variant_07
public void test_apply_variant_07()
Variant overlapping exon end
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test_apply_variant_08
public void test_apply_variant_08()
Variant right after exon end
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test_apply_variant_09
public void test_apply_variant_09()
Variant after exon end
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test_apply_variant_10
public void test_apply_variant_10()
Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exon
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test_apply_variant_11
public void test_apply_variant_11()
Variant over exon: variant is larger than exon and starts right at exons start and ends after exon end
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test_apply_variant_12
public void test_apply_variant_12()
Variant over exon: variant is larger than exon, starts before exon start and end right at exon end
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test_apply_variant_13
public void test_apply_variant_13()
Variant over exon: variant is on the same coordiantes as exon
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