Class TestCasesIntegrationApply
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationApply
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public class TestCasesIntegrationApply extends TestCasesIntegrationBase
Test 'apply' method (apply variant to marker)- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description static int
SHOW_EVERY
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Fields 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 Constructor Description TestCasesIntegrationApply()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
test_01_Exon_SNPs()
Test 'apply' on exons (test sequence changes) Only using SNPs variantsvoid
test_02_Exon_INS()
Test 'apply' on exons (test sequence changes) Only using insertion variantsvoid
test_03_Exon_DEL()
Test 'apply' on exons (test sequence changes) Only using deletions variantsvoid
test_04_Exon_MNP()
Test 'apply' on exons (test sequence changes) Only using deletions variantsvoid
test_apply_05_delete_whole_exon()
Exon completely removed by a deletion.void
test_apply_06_delete_upstream()
Upstream region is completely removed by a deletion.void
test_apply_07_delete_upstream()
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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Method Detail
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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
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test_02_Exon_INS
@Test public void test_02_Exon_INS()
Test 'apply' on exons (test sequence changes) Only using insertion variants
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test_03_Exon_DEL
@Test public void test_03_Exon_DEL()
Test 'apply' on exons (test sequence changes) Only using deletions variants
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test_04_Exon_MNP
@Test public void test_04_Exon_MNP()
Test 'apply' on exons (test sequence changes) Only using deletions variants
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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
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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
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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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