Class TestCasesIntegrationVariant
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationVariant
Test cases for variants
- Author:
- pcingola
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Field Summary
Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
BASE_DIR, debug, ignoreErrors, prefixes, shiftHgvs, SHOW_EVERY, testsDir, testType, verbose
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
test_08()
CDS test (CDS = CoDing Sequences) Build CDS form exon sequencesvoid
test_09()
Test SNP effect predictor for a transcriptvoid
test_11()
Test SNP effect predictor: Test UTR distances, Up/Downstream distancesvoid
test_12()
Test SNP effect predictor: Test Splice sitesvoid
Test SNP effect predictor: Test Splice sites (make sure they are only 2 bases long)void
test_19()
Test SNP effect predictor: Test start codon gainedvoid
test_20()
Test SNP effect predictor: Test start codon gained (reverse strand)void
test_21()
Test SNP effect predictor for a transcript (Insertions)void
Test SNP effect predictor for a transcript (Insertions)void
Test SNP effect predictor for a transcript (Insertions)void
test_22()
Read file test: Should throw an exception (chromosome not found)void
Test SNP effect predictor for a transcript (Insertions)void
Test SNP effect predictor for a transcript (Insertions)void
void
Test SNP effect predictor for a transcript (Insertions)void
Splice site: Bug reported by Wang, Xushengvoid
Test effect when hits a gene, but not any transcript within a gene.void
Rare Amino acidvoid
MT chromo Effectusing an alternative codon table: Codon change : atA / atG Standard codon table : Ile / Met => NON_SYNONYMOUS Mithocondria codon table: Met / Met => SYNONYMOUSvoid
Start gainedvoid
Not start gainedvoid
Start gainedvoid
Not start gainedvoid
Make sure all variant effects have appropriate impactsvoid
TestMethods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
applyTranscript, before, build, buildAndCompare, buildEmbl, buildGeneBank, buildGeneBank, buildGetBuildCmd, buildGff3AndCompare, buildGtfAndCompare, checkHgvs, checkNoChange, checkTranscriptError, compareHgvs, compareHgvs, compareVep, compareVepSO, init, loadSnpEffectPredictor, path, pathClassName, pathMigrate, showTranscripts, showTranscripts, snpEffect, snpEffect, snpEffectCancer
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Constructor Details
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TestCasesIntegrationVariant
public TestCasesIntegrationVariant()
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Method Details
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test_08
@Test public void test_08()CDS test (CDS = CoDing Sequences) Build CDS form exon sequences -
test_09
@Test public void test_09()Test SNP effect predictor for a transcript -
test_11
@Test public void test_11()Test SNP effect predictor: Test UTR distances, Up/Downstream distances -
test_12
@Test public void test_12()Test SNP effect predictor: Test Splice sites -
test_12_2
@Test public void test_12_2()Test SNP effect predictor: Test Splice sites (make sure they are only 2 bases long) -
test_19
@Test public void test_19()Test SNP effect predictor: Test start codon gained -
test_20
@Test public void test_20()Test SNP effect predictor: Test start codon gained (reverse strand) -
test_21
@Test public void test_21()Test SNP effect predictor for a transcript (Insertions) -
test_21_2
@Test public void test_21_2()Test SNP effect predictor for a transcript (Insertions) -
test_21_3
@Test public void test_21_3()Test SNP effect predictor for a transcript (Insertions) -
test_22
@Test public void test_22()Read file test: Should throw an exception (chromosome not found) -
test_23_MNP_on_exon_edge
@Test public void test_23_MNP_on_exon_edge()Test SNP effect predictor for a transcript (Insertions) -
test_24_delete_exon_utr
@Test public void test_24_delete_exon_utr()Test SNP effect predictor for a transcript (Insertions) -
test_25_exon_bases
@Test public void test_25_exon_bases() -
test_26_chr15_78909452
@Test public void test_26_chr15_78909452()Test SNP effect predictor for a transcript (Insertions) -
test_28_Splice_mm37_ENSMUSG00000005763
@Test public void test_28_Splice_mm37_ENSMUSG00000005763()Splice site: Bug reported by Wang, Xusheng -
test_29_Intergenic_in_Gene
@Test public void test_29_Intergenic_in_Gene()Test effect when hits a gene, but not any transcript within a gene. This is an extremely weird case, might be an annotation problem. -
test_30_RareAa
@Test public void test_30_RareAa()Rare Amino acid -
test_31_CodonTable
@Test public void test_31_CodonTable()MT chromo Effectusing an alternative codon table: Codon change : atA / atG Standard codon table : Ile / Met => NON_SYNONYMOUS Mithocondria codon table: Met / Met => SYNONYMOUS -
test_32_StartGained
@Test public void test_32_StartGained()Start gained -
test_33_StartGained_NOT
@Test public void test_33_StartGained_NOT()Not start gained -
test_34_StartGained
@Test public void test_34_StartGained()Start gained -
test_35_StartGained_NOT
@Test public void test_35_StartGained_NOT()Not start gained -
test_36_EffectImpact
@Test public void test_36_EffectImpact()Make sure all variant effects have appropriate impacts -
test_38_NON_SYNONYMOUS_START
@Test public void test_38_NON_SYNONYMOUS_START()Test
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