Class TestCasesHgvsDnaDup
- java.lang.Object
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- org.snpeff.snpEffect.testCases.unity.TestCasesBase
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- org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup
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public class TestCasesHgvsDnaDup extends TestCasesBase
Test case
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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 TestCasesHgvsDnaDup()
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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()
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.5dupT (or g.5dup, not g.5_6insT) denotes a duplication ("insertion") of the T nucleotide at position 5 in the genomic reference sequence changing ACTCTGTGCC to ACTCTTGTGCCvoid
test_04()
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.7dupT (or g.7dup, not g.5dupT, not g.7_8insT) denotes a duplication ("insertion") of the T nucleotide at position 7 in the genomic reference sequence changing AGACTTTGTGCC to AGACTTTTGTGCCvoid
test_05()
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.7_8dup (or g.7_8dupTG, not g.5_6dup, not g.8_9insTG) denotes a TG duplication in the TG-tandem repeat sequence changing ACTTTGTGCC to ACTTTGTGTGCCvoid
test_06()
void
test_07()
Duplication with variant shifted towards 3-primevoid
test_08()
Duplication with variant shifted towards 3-primevoid
test_09()
Dup in intronvoid
test_10()
Dup in exon-intron boundaryvoid
test_11()
Dup in intron-exon boundary-
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, prependSequenceToFirstExon, showTranscripts
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Method Detail
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init
protected void init()
- Overrides:
init
in classTestCasesBase
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test_01
public void test_01()
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test_02
public void test_02()
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test_03
public void test_03()
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.5dupT (or g.5dup, not g.5_6insT) denotes a duplication ("insertion") of the T nucleotide at position 5 in the genomic reference sequence changing ACTCTGTGCC to ACTCTTGTGCC
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test_04
public void test_04()
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.7dupT (or g.7dup, not g.5dupT, not g.7_8insT) denotes a duplication ("insertion") of the T nucleotide at position 7 in the genomic reference sequence changing AGACTTTGTGCC to AGACTTTTGTGCC
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test_05
public void test_05()
Test case from http://www.hgvs.org/mutnomen/recs-DNA.html g.7_8dup (or g.7_8dupTG, not g.5_6dup, not g.8_9insTG) denotes a TG duplication in the TG-tandem repeat sequence changing ACTTTGTGCC to ACTTTGTGTGCC
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test_06
public void test_06()
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test_07
public void test_07()
Duplication with variant shifted towards 3-prime
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test_08
public void test_08()
Duplication with variant shifted towards 3-prime
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test_09
public void test_09()
Dup in intron
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test_10
public void test_10()
Dup in exon-intron boundary
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test_11
public void test_11()
Dup in intron-exon boundary
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