Class TestCasesIntegrationMotif
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
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public class TestCasesIntegrationMotif extends TestCasesIntegrationBase
Test Motif databases- Author:
- pcingola
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Field Summary
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Fields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
debug, ignoreErrors, shiftHgvs, SHOW_EVERY, testsDir, verbose
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Constructor Summary
Constructors Constructor Description TestCasesIntegrationMotif()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01()
void
test_01_ann()
void
test_02()
void
test_02_ann()
void
test_03()
void
test_03_ann()
void
test_04()
MNP outside Motif: Should not throw any exceptionvoid
test_05()
Motif has 9 bases but ENSEMBL file marks it as a 10 base interval SNP affect last base (as marked by ENSEMBL), since there is no sequence for that base position, an exception is thrown.-
Methods inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
appyTranscript, build, buildAndCompare, buildEmbl, buildGeneBank, buildGff3AndCompare, buildGtfAndCompare, checkHgvs, checkNoChange, checkTranscriptError, compareHgvs, compareHgvs, compareVep, compareVepSO, init, loadSnpEffectPredictor, showTranscripts, showTranscripts, snpEffect, snpEffect, snpEffectCancer
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Method Detail
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test_01
public void test_01()
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test_01_ann
public void test_01_ann()
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test_02
public void test_02()
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test_02_ann
public void test_02_ann()
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test_03
public void test_03()
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test_03_ann
public void test_03_ann()
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test_04
public void test_04()
MNP outside Motif: Should not throw any exception
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test_05
public void test_05()
Motif has 9 bases but ENSEMBL file marks it as a 10 base interval SNP affect last base (as marked by ENSEMBL), since there is no sequence for that base position, an exception is thrown.
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