Commit 048dc6d5 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Style

parent 860ab6c3
......@@ -4,12 +4,12 @@ package nl.lumc.sasc.biopet.extensions.clever
* Created by wyleung on 4-4-16.
*/
import java.io.{File, PrintWriter}
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import nl.lumc.sasc.biopet.utils.ToolCommand
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
import scala.io.Source
......@@ -125,9 +125,9 @@ object CleverFixVCF extends ToolCommand {
val inputVCF = Source.fromFile(input)
val writer = new PrintWriter(output)
inputVCF.getLines().foreach(x =>
writer.write(replaceHeaderLine(x, vcfColHeader, vcfColReplacementHeader + commandArgs.sampleLabel, extraHeader))
)
inputVCF.getLines().foreach(x =>
writer.write(replaceHeaderLine(x, vcfColHeader, vcfColReplacementHeader + commandArgs.sampleLabel, extraHeader))
)
writer.close()
inputVCF.close()
}
......
......@@ -5,8 +5,8 @@ import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
* Created by wyleung on 13-5-16.
*/
* Created by wyleung on 13-5-16.
*/
class CleverFixVCFTest extends TestNGSuite with Matchers {
@Test
......@@ -16,10 +16,9 @@ class CleverFixVCFTest extends TestNGSuite with Matchers {
CleverFixVCF.vcfColHeader,
CleverFixVCF.vcfColReplacementHeader + "testsample",
CleverFixVCF.extraHeader
) should equal(CleverFixVCF.extraHeader + "\n" + CleverFixVCF.vcfColReplacementHeader + "testsample"+ "\n")
) should equal(CleverFixVCF.extraHeader + "\n" + CleverFixVCF.vcfColReplacementHeader + "testsample" + "\n")
}
@Test
def replacementOther = {
val vcfRecord = "chrM\t312\tL743020\t.\t<DEL>\t.\tPASS\tBPWINDOW=313,16189;CILEN=15866,15888;IMPRECISE;SVLEN=-15877;SVTYPE=DEL\tGT:DP\t1/.:103"
......@@ -29,7 +28,7 @@ class CleverFixVCFTest extends TestNGSuite with Matchers {
CleverFixVCF.vcfColHeader,
CleverFixVCF.vcfColReplacementHeader + "testsample",
CleverFixVCF.extraHeader
) should equal(vcfRecordExpected+ "\n")
) should equal(vcfRecordExpected + "\n")
}
}
......@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.extensions.breakdancer.{BreakdancerCaller, BreakdancerConfig, BreakdancerVCF}
import nl.lumc.sasc.biopet.extensions.breakdancer.{ BreakdancerCaller, BreakdancerConfig, BreakdancerVCF }
import nl.lumc.sasc.biopet.extensions.picard.SortVcf
import nl.lumc.sasc.biopet.utils.config.Configurable
......
......@@ -15,7 +15,7 @@
*/
package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import nl.lumc.sasc.biopet.extensions.clever.{CleverCaller, CleverFixVCF}
import nl.lumc.sasc.biopet.extensions.clever.{ CleverCaller, CleverFixVCF }
import nl.lumc.sasc.biopet.extensions.picard.SortVcf
import nl.lumc.sasc.biopet.utils.config.Configurable
......
......@@ -30,7 +30,7 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
var inputBams: Map[String, File] = Map.empty
val sampleNameSuffix: String = config("samplename_suffix", default="")
val sampleNameSuffix: String = config("samplename_suffix", default = "")
def outputVCF(sample: String): Option[File] = {
outputVCFs.get(sample) match {
......
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