Commit 3ce0cd9f authored by Sander Bollen's avatar Sander Bollen
Browse files

autostyle

parent 8e13d8ac
...@@ -33,7 +33,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver ...@@ -33,7 +33,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/cnmops.R") protected var script: File = new File("/nl/lumc/sasc/biopet/extensions/cnmops.R")
def versionCommand = super.cmdLine + "--version" def versionCommand = super.cmdLine + "--version"
def versionRegex = "\\d+\\.\\d+\\.\\d+".r def versionRegex = "\\d+\\.\\d+\\.\\d+".r
private def stringToInt(s: String): Option[Int] = { private def stringToInt(s: String): Option[Int] = {
try { try {
...@@ -44,10 +44,10 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver ...@@ -44,10 +44,10 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
} }
/** /**
* Check whether version of cn mops is at least 1.18.0 * Check whether version of cn mops is at least 1.18.0
* *
* @return * @return
*/ */
def versionCheck: Boolean = { def versionCheck: Boolean = {
getVersion match { getVersion match {
case Some(version) => { case Some(version) => {
...@@ -79,7 +79,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver ...@@ -79,7 +79,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy val outputCnv: File = { lazy val outputCnv: File = {
outputDir match { outputDir match {
case Some(dir) if dir.exists => new File(dir, "cnv.txt") case Some(dir) if dir.exists => new File(dir, "cnv.txt")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNV output") case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNV output")
} }
} }
...@@ -87,7 +87,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver ...@@ -87,7 +87,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy val outputCnr: File = { lazy val outputCnr: File = {
outputDir match { outputDir match {
case Some(dir) if dir.exists => new File(dir, "cnr.txt") case Some(dir) if dir.exists => new File(dir, "cnr.txt")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNR output") case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS CNR output")
} }
} }
...@@ -95,7 +95,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver ...@@ -95,7 +95,7 @@ class Cnmops(val root: Configurable) extends RscriptCommandLineFunction with Ver
lazy val rawOutput: File = { lazy val rawOutput: File = {
outputDir match { outputDir match {
case Some(dir) if dir.exists => new File(dir, "rawoutput.txt") case Some(dir) if dir.exists => new File(dir, "rawoutput.txt")
case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS raw output") case _ => throw new IllegalArgumentException("Unexpected error when trying to set cn.MOPS raw output")
} }
} }
......
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