Commit 942ad5e7 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added unit test

parent 77eae709
@r01_filter hello
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@r03_filter
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@r01_filter hello
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@r02
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@r03_filter
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@r04
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/**
* Biopet is built on top of GATK Queue for building bioinformatic
* pipelines. It is mainly intended to support LUMC SHARK cluster which is running
* SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
* should also be able to execute Biopet tools and pipelines.
*
* Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
*
* Contact us at: sasc@lumc.nl
*
* A dual licensing mode is applied. The source code within this project is freely available for non-commercial use under an AGPL
* license; For commercial users or users who do not want to follow the AGPL
* license, please contact us to obtain a separate license.
*/
package nl.lumc.sasc.biopet.tools
import java.io.File
import java.nio.file.Paths
import org.scalatest.Matchers
import org.scalatest.mock.MockitoSugar
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
import scala.io.Source
/**
* Created by ahbbollen on 27-8-15.
*/
class FastqFilterTest extends TestNGSuite with MockitoSugar with Matchers {
import FastqFilter._
private def resourcePath(p: String): String = {
Paths.get(getClass.getResource(p).toURI).toString
}
val preFilterFastq = resourcePath("/paired01_pre_filter.fq")
val postFilterFastq = resourcePath("/paired01_post_filter.fq")
@Test
def testMain() = {
val temp = File.createTempFile("out", ".fastq")
temp.deleteOnExit()
val args = Array("-I", preFilterFastq, "-o", temp.getAbsolutePath, "--idRegex", "_filter$")
main(args)
Source.fromFile(temp).getLines().toList shouldBe Source.fromFile(postFilterFastq).getLines().toList
}
}
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