Class TestCasesApplyDel
java.lang.Object
org.snpeff.snpEffect.testCases.unity.TestCasesBase
org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel
Test cases: apply a variant (DEL) to a transcript
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Field Summary
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 -
Method Summary
Modifier and TypeMethodDescriptionvoid
Variant before exonvoid
Variant right before exon startvoid
Variant overlapping exon startvoid
Variant at exon startvoid
Variant in exonvoid
Variant right before exon endvoid
Variant overlapping exon endvoid
Variant right after exon endvoid
Variant after exon endvoid
Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exonvoid
Variant over exon: variant is larger than exon and starts right at exons start and ends after exon endvoid
Variant over exon: variant is larger than exon, starts before exon start and end right at exon endvoid
Variant over exon: variant is on the same coordiantes as exonMethods inherited from class org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply
initSnpEffPredictor
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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Constructor Details
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TestCasesApplyDel
public TestCasesApplyDel()
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Method Details
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test_apply_variant_01
@Test public void test_apply_variant_01()Variant before exon -
test_apply_variant_02
@Test public void test_apply_variant_02()Variant right before exon start -
test_apply_variant_03
@Test public void test_apply_variant_03()Variant overlapping exon start -
test_apply_variant_04
@Test public void test_apply_variant_04()Variant at exon start -
test_apply_variant_05
@Test public void test_apply_variant_05()Variant in exon -
test_apply_variant_06
@Test public void test_apply_variant_06()Variant right before exon end -
test_apply_variant_07
@Test public void test_apply_variant_07()Variant overlapping exon end -
test_apply_variant_08
@Test public void test_apply_variant_08()Variant right after exon end -
test_apply_variant_09
@Test public void test_apply_variant_09()Variant after exon end -
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 -
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 -
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 -
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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