Class TestCasesIntegrationApply
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
Test 'apply' method (apply variant to marker)
- Author:
- pcingola
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Field Summary
FieldsFields inherited from class org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
BASE_DIR, debug, ignoreErrors, prefixes, shiftHgvs, testsDir, testType, verbose
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Test 'apply' on exons (test sequence changes) Only using SNPs variantsvoid
Test 'apply' on exons (test sequence changes) Only using insertion variantsvoid
Test 'apply' on exons (test sequence changes) Only using deletions variantsvoid
Test 'apply' on exons (test sequence changes) Only using deletions variantsvoid
Exon completely removed by a deletion.void
Upstream region is completely removed by a deletion.void
Upstream region is completely removed by a deletion.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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Field Details
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SHOW_EVERY
public static int SHOW_EVERY
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Constructor Details
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TestCasesIntegrationApply
public TestCasesIntegrationApply()
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Method Details
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test_01_Exon_SNPs
@Test public void test_01_Exon_SNPs()Test 'apply' on exons (test sequence changes) Only using SNPs variants -
test_02_Exon_INS
@Test public void test_02_Exon_INS()Test 'apply' on exons (test sequence changes) Only using insertion variants -
test_03_Exon_DEL
@Test public void test_03_Exon_DEL()Test 'apply' on exons (test sequence changes) Only using deletions variants -
test_04_Exon_MNP
@Test public void test_04_Exon_MNP()Test 'apply' on exons (test sequence changes) Only using deletions variants -
test_apply_05_delete_whole_exon
@Test public void test_apply_05_delete_whole_exon()Exon completely removed by a deletion. Bug triggers a null pointer on 'Transcript.apply()': Fixed -
test_apply_06_delete_upstream
@Test public void test_apply_06_delete_upstream()Upstream region is completely removed by a deletion. Bug triggers a null pointer: Fixed -
test_apply_07_delete_upstream
@Test public void test_apply_07_delete_upstream()Upstream region is completely removed by a deletion. Bug triggers a null pointer: Fixed
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