Class TestCasesApplyDel
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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.TestCasesApplyDel
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public class TestCasesApplyDel extends TestCasesBaseApply
Test cases: apply a variant (DEL) to a transcript
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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 TestCasesApplyDel()
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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 right before exon startvoid
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 right before exon endvoid
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, path, pathClassName, prependSequenceToFirstExon
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Method Detail
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test_apply_variant_01
@Test public void test_apply_variant_01()
Variant before exon
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test_apply_variant_02
@Test public void test_apply_variant_02()
Variant right before exon start
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test_apply_variant_03
@Test public void test_apply_variant_03()
Variant overlapping exon start
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test_apply_variant_04
@Test public void test_apply_variant_04()
Variant at exon start
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test_apply_variant_05
@Test public void test_apply_variant_05()
Variant in exon
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test_apply_variant_06
@Test public void test_apply_variant_06()
Variant right before exon end
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test_apply_variant_07
@Test public void test_apply_variant_07()
Variant overlapping exon end
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test_apply_variant_08
@Test public void test_apply_variant_08()
Variant right after exon end
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test_apply_variant_09
@Test public void test_apply_variant_09()
Variant after exon end
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test_apply_variant_10
@Test 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
@Test 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
@Test 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
@Test public void test_apply_variant_13()
Variant over exon: variant is on the same coordiantes as exon
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