Class IntegrationTest
- java.lang.Object
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- org.snpeff.snpEffect.testCases.integration.TestCasesIntegrationBase
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- org.snpeff.snpEffect.testCases.integration.IntegrationTest
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- Direct Known Subclasses:
TestCasesIntegrationSnpEff
,TestCasesIntegrationSnpEffMultiThread
public class IntegrationTest extends TestCasesIntegrationBase
Base class for integration tests- Author:
- pcingola
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Field Summary
Fields Modifier and Type Field Description int
BUFFER_SIZE
static int
MAX_LINES_DIFF
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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 Constructor Description IntegrationTest()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description java.lang.String
command(CommandLine command)
Run a 'command' and return everything printed to stdoutvoid
command(CommandLine command, java.lang.String expectedOutputFile)
Run a command and compare to an expected output (form a file)java.lang.String
showCommand(CommandLine command)
Show command (as a command line)java.lang.String
showDiff(java.lang.String s1, java.lang.String s2)
Show the difference between who string (multi-line strings)java.lang.String
showDiffLine(java.lang.String l1, java.lang.String l2)
Show difference between two lines-
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 Detail
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MAX_LINES_DIFF
public static final int MAX_LINES_DIFF
- See Also:
- Constant Field Values
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BUFFER_SIZE
public final int BUFFER_SIZE
- See Also:
- Constant Field Values
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Method Detail
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command
public java.lang.String command(CommandLine command)
Run a 'command' and return everything printed to stdout
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command
public void command(CommandLine command, java.lang.String expectedOutputFile)
Run a command and compare to an expected output (form a file)
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showCommand
public java.lang.String showCommand(CommandLine command)
Show command (as a command line)
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showDiff
public java.lang.String showDiff(java.lang.String s1, java.lang.String s2)
Show the difference between who string (multi-line strings)
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showDiffLine
public java.lang.String showDiffLine(java.lang.String l1, java.lang.String l2)
Show difference between two lines
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