Package org.snpeff.snpEffect.testCases.unity

Class TestCasesHgvsDnaDup

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

org.snpeff.snpEffect.testCases.unity.TestCasesHgvsDnaDup

public class TestCasesHgvsDnaDup
extends TestCasesBase

Test case

Field Summary

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

Constructor Summary

Constructors

Constructor	Description
TestCasesHgvsDnaDup()

Method Summary

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 ACTCTTGTGCC
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
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
void	test_06()
void	test_07()	Duplication with variant shifted towards 3-prime
void	test_08()	Duplication with variant shifted towards 3-prime
void	test_09()	Dup in intron
void	test_10()	Dup in exon-intron boundary
void	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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TestCasesHgvsDnaDup

public TestCasesHgvsDnaDup()

Method Detail

init

protected void init()

Overrides:

init in class TestCasesBase

test_01

public void test_01()

test_02

public void test_02()

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

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

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

test_06

public void test_06()

test_07

public void test_07()

Duplication with variant shifted towards 3-prime

test_08

public void test_08()

Duplication with variant shifted towards 3-prime

test_09

public void test_09()

Dup in intron

test_10

public void test_10()

Dup in exon-intron boundary

test_11

public void test_11()

Dup in intron-exon boundary