Class IntegrationTest
java.lang.Object
org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
org.snpeff.snpEffect.testCases.integration.IntegrationTest
- Direct Known Subclasses:
TestCasesIntegrationSnpEff
,TestCasesIntegrationSnpEffMultiThread
Base class for integration tests
- Author:
- pcingola
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Field Summary
FieldsFields 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 TypeMethodDescriptioncommand
(CommandLine command) Run a 'command' and return everything printed to stdoutvoid
command
(CommandLine command, String expectedOutputFile) Run a command and compare to an expected output (form a file)showCommand
(CommandLine command) Show command (as a command line)Show the difference between who string (multi-line strings)showDiffLine
(String l1, String l2) Show difference between two linesMethods 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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MAX_LINES_DIFF
public static final int MAX_LINES_DIFF- See Also:
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BUFFER_SIZE
public final int BUFFER_SIZE- See Also:
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Constructor Details
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IntegrationTest
public IntegrationTest()
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Method Details
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command
Run a 'command' and return everything printed to stdout -
command
Run a command and compare to an expected output (form a file) -
showCommand
Show command (as a command line) -
showDiff
Show the difference between who string (multi-line strings) -
showDiffLine
Show difference between two lines
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