Commit e5ac93ab authored by Sander Bollen's avatar Sander Bollen
Browse files

style fixes

parent c3da88c0
......@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Output }
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
def analysis_type = "DepthOfCoverage"
......@@ -26,7 +26,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
new File(out + "_summary")
}
lazy val statisticsFile:File = {
lazy val statisticsFile: File = {
new File(out + "_statistics")
}
......@@ -117,7 +117,6 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Argument(required = false)
var printBinEndpointsAndExit: Boolean = false
override def cmdLine = {
super.cmdLine + required("--out", out) +
optional("--calculateCoverageOverGenes", calculateCoveraOverGenes) +
......
package nl.lumc.sasc.biopet.extensions.xhmm
import nl.lumc.sasc.biopet.core.{BiopetCommandLineFunction, Version}
import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
/**
* Created by Sander Bollen on 23-11-16.
*
* Generic abstract class for XHMM commands
*/
abstract class Xhmm extends BiopetCommandLineFunction with Version {
* Created by Sander Bollen on 23-11-16.
*
* Generic abstract class for XHMM commands
*/
abstract class Xhmm extends BiopetCommandLineFunction with Version {
executable = config("exe", namespace = "xhmm", default = "xhmm")
......
......@@ -4,13 +4,13 @@ import java.io.File
import nl.lumc.sasc.biopet.core.summary.Summarizable
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
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
@Input
......@@ -53,7 +53,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
map(x => XcnvLine(x(0), x(1), x(2))).toList
val samples = lines.map(_.sample)
samples.map{x =>
samples.map { x =>
val sampleLines = lines.filter(_.sample == x)
x -> Map(
"DEL" -> sampleLines.count(_.cnvType == "DEL"),
......
......@@ -4,11 +4,11 @@ import java.io.File
import nl.lumc.sasc.biopet.core.Reference
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 }
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
@Input
......@@ -24,7 +24,7 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
var r: File = _
@Argument
var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
var discoverParamsFile: File = config("discover_params", namespace = "xhmm")
def cmdLine = {
executable + required("--genotype") +
......@@ -36,6 +36,4 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
required("-v", outputVcf)
}
}
......@@ -3,12 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File
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 }
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmMatrix(val root: Configurable) extends Xhmm {
@Input
......
......@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmMergeGatkDepths(val root: Configurable) extends Xhmm {
@Input(doc = "List of input depths files")
......
......@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File
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 }
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmNormalize(val root: Configurable) extends Xhmm {
@Input
......
......@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmPca(val root: Configurable) extends Xhmm {
@Input
......
......@@ -9,8 +9,8 @@ import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmTest extends TestNGSuite with Matchers {
@Test
......
......@@ -15,9 +15,9 @@
package nl.lumc.sasc.biopet.pipelines.kopisu
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference}
import nl.lumc.sasc.biopet.pipelines.kopisu.methods.{CnmopsMethod, ConiferMethod, FreecMethod, XhmmMethod}
import nl.lumc.sasc.biopet.utils.{BamUtils, Logging}
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference }
import nl.lumc.sasc.biopet.pipelines.kopisu.methods.{ CnmopsMethod, ConiferMethod, FreecMethod, XhmmMethod }
import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.queue.QScript
......@@ -75,7 +75,7 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
add(method)
}
xhmmMethod.foreach{ method =>
xhmmMethod.foreach { method =>
method.inputBams = inputBams
method.outputDir = new File(outputDir, "xhmm_methid")
}
......
......@@ -6,8 +6,8 @@ import nl.lumc.sasc.biopet.extensions.xhmm._
import nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
def name = "xhmm"
......
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