Commit 13689911 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix compile errors

parent bb300878
......@@ -38,8 +38,8 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
def defaultThreads = 1
var vmem: Option[String] = config("vmem")
protected def defaultCoreMemory: Double = 1.0
protected def defaultVmemFactor: Double = 1.4
def defaultCoreMemory: Double = 1.0
def defaultVmemFactor: Double = 1.4
var vmemFactor: Double = config("vmem_factor", default = defaultVmemFactor)
var residentFactor: Double = config("resident_factor", default = 1.2)
......@@ -150,13 +150,13 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
}
/** Command to get version of executable */
protected def versionCommand: String = null
protected[core] def versionCommand: String = null
/** Regex to get version from version command output */
protected def versionRegex: Regex = null
protected[core] def versionRegex: Regex = null
/** Allowed exit codes for the version command */
protected def versionExitcode = List(0)
protected[core] def versionExitcode = List(0)
/** Executes the version command */
private[core] def getVersionInternal: Option[String] = {
......
......@@ -25,7 +25,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
javaGCTimeLimit = config("java_gc_timelimit")
override protected def defaultVmemFactor: Double = 2.0
override def defaultVmemFactor: Double = 2.0
/** Constructs java opts, this adds scala threads */
override def javaOpts = super.javaOpts +
......
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