Class TestCasesIntegrationMotif
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationMotif
Test Motif databases
- 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_01()
void
void
test_02()
void
void
test_03()
void
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
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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TestCasesIntegrationMotif
public TestCasesIntegrationMotif()
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Method Details
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test_01
@Test public void test_01() -
test_01_ann
@Test public void test_01_ann() -
test_02
@Test public void test_02() -
test_02_ann
@Test public void test_02_ann() -
test_03
@Test public void test_03() -
test_03_ann
@Test public void test_03_ann() -
test_04
@Test public void test_04()MNP outside Motif: Should not throw any exception -
test_05
@Test 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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