Package org.snpeff.snpEffect.testCases.unity

Class TestCasesApplyDel

java.lang.Object

org.snpeff.snpEffect.testCases.unity.TestCasesBase

org.snpeff.snpEffect.testCases.unity.TestCasesBaseApply

org.snpeff.snpEffect.testCases.unity.TestCasesApplyDel

public class TestCasesApplyDel
extends TestCasesBaseApply

Test cases: apply a variant (DEL) to a transcript

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
TestCasesApplyDel()

Method Summary

Modifier and Type	Method	Description
void	test_apply_variant_01()	Variant before exon
void	test_apply_variant_02()	Variant right before exon start
void	test_apply_variant_03()	Variant overlapping exon start
void	test_apply_variant_04()	Variant at exon start
void	test_apply_variant_05()	Variant in exon
void	test_apply_variant_06()	Variant right before exon end
void	test_apply_variant_07()	Variant overlapping exon end
void	test_apply_variant_08()	Variant right after exon end
void	test_apply_variant_09()	Variant after exon end
void	test_apply_variant_10()	Variant over exon: variant is larger than exon, starts before exon and overlaps the whole exon
void	test_apply_variant_11()	Variant over exon: variant is larger than exon and starts right at exons start and ends after exon end
void	test_apply_variant_12()	Variant over exon: variant is larger than exon, starts before exon start and end right at exon end
void	test_apply_variant_13()	Variant over exon: variant is on the same coordiantes as exon

Methods 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, prependSequenceToFirstExon, showTranscripts

Methods inherited from class java.lang.Object

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

Constructor Detail

TestCasesApplyDel

public TestCasesApplyDel()

Method Detail

test_apply_variant_01

public void test_apply_variant_01()

Variant before exon

test_apply_variant_02

public void test_apply_variant_02()

Variant right before exon start

test_apply_variant_03

public void test_apply_variant_03()

Variant overlapping exon start

test_apply_variant_04

public void test_apply_variant_04()

Variant at exon start

test_apply_variant_05

public void test_apply_variant_05()

Variant in exon

test_apply_variant_06

public void test_apply_variant_06()

Variant right before exon end

test_apply_variant_07

public void test_apply_variant_07()

Variant overlapping exon end

test_apply_variant_08

public void test_apply_variant_08()

Variant right after exon end

test_apply_variant_09

public void test_apply_variant_09()

Variant after exon end

test_apply_variant_10

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

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

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

public void test_apply_variant_13()

Variant over exon: variant is on the same coordiantes as exon