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, 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 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, path, pathClassName, prependSequenceToFirstExon
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Method Detail
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init
protected void init()
- Overrides:
init
in classTestCasesBase
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test_01
@Test public void test_01()
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test_02
@Test public void test_02()
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test_03
@Test 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
@Test 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
@Test 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
@Test public void test_06()
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test_07
@Test public void test_07()
Duplication with variant shifted towards 3-prime
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test_08
@Test public void test_08()
Duplication with variant shifted towards 3-prime
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test_09
@Test public void test_09()
Dup in intron
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test_10
@Test public void test_10()
Dup in exon-intron boundary
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test_11
@Test public void test_11()
Dup in intron-exon boundary
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