Class TestCasesApplyMixed
- 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.TestCasesApplyMixed
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public class TestCasesApplyMixed extends TestCasesBaseApply
Test cases: apply a variant (MIXED) 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 TestCasesApplyMixed()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_apply_variant_01_longer()
Variant before exonvoid
test_apply_variant_01_shorter()
Variant before exonvoid
test_apply_variant_02_longer()
Variant before exonvoid
test_apply_variant_02_shorter()
Variant before exonvoid
test_apply_variant_03_longer()
Variant overlapping exon startvoid
test_apply_variant_03_shorter()
Variant overlapping exon startvoid
test_apply_variant_04_longer()
Variant at exon startvoid
test_apply_variant_04_shorter()
Variant at exon startvoid
test_apply_variant_05_longer()
Variant in exonvoid
test_apply_variant_05_shorter()
Variant in exonvoid
test_apply_variant_06_longer()
Variant in exonvoid
test_apply_variant_06_shorter()
Variant in exonvoid
test_apply_variant_07_longer()
Variant overlapping exon endvoid
test_apply_variant_07_shorter()
Variant overlapping exon endvoid
test_apply_variant_08_longer()
Variant right after exon endvoid
test_apply_variant_08_shorter()
Variant right after exon endvoid
test_apply_variant_09_longer()
Variant after exon endvoid
test_apply_variant_09_shorter()
Variant after exon end-
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_shorter
public void test_apply_variant_01_shorter()
Variant before exon
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test_apply_variant_01_longer
public void test_apply_variant_01_longer()
Variant before exon
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test_apply_variant_02_shorter
public void test_apply_variant_02_shorter()
Variant before exon
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test_apply_variant_02_longer
public void test_apply_variant_02_longer()
Variant before exon
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test_apply_variant_03_shorter
public void test_apply_variant_03_shorter()
Variant overlapping exon start
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test_apply_variant_03_longer
public void test_apply_variant_03_longer()
Variant overlapping exon start
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test_apply_variant_04_shorter
public void test_apply_variant_04_shorter()
Variant at exon start
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test_apply_variant_04_longer
public void test_apply_variant_04_longer()
Variant at exon start
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test_apply_variant_05_shorter
public void test_apply_variant_05_shorter()
Variant in exon
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test_apply_variant_05_longer
public void test_apply_variant_05_longer()
Variant in exon
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test_apply_variant_06_shorter
public void test_apply_variant_06_shorter()
Variant in exon
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test_apply_variant_06_longer
public void test_apply_variant_06_longer()
Variant in exon
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test_apply_variant_07_shorter
public void test_apply_variant_07_shorter()
Variant overlapping exon end
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test_apply_variant_07_longer
public void test_apply_variant_07_longer()
Variant overlapping exon end
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test_apply_variant_08_shorter
public void test_apply_variant_08_shorter()
Variant right after exon end
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test_apply_variant_08_longer
public void test_apply_variant_08_longer()
Variant right after exon end
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test_apply_variant_09_shorter
public void test_apply_variant_09_shorter()
Variant after exon end
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test_apply_variant_09_longer
public void test_apply_variant_09_longer()
Variant after exon end
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