Commit 14fe91d9 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Remove unused function

parent 6c8f5376
...@@ -307,25 +307,5 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript { ...@@ -307,25 +307,5 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
} }
object Mapping extends PipelineCommand { object Mapping extends PipelineCommand {
def loadFromLibraryConfig(root: Configurable, runConfig: Map[String, Any], sampleConfig: Map[String, Any],
runDir: String, startJobs: Boolean = true): Mapping = {
val mapping = new Mapping(root)
logger.debug("Mapping runconfig: " + runConfig)
if (runConfig.contains("R1")) mapping.input_R1 = new File(runConfig("R1").toString)
if (runConfig.contains("R2")) mapping.input_R2 = new File(runConfig("R2").toString)
mapping.paired = (mapping.input_R2 != null)
mapping.RGLB = runConfig("ID").toString
mapping.RGSM = sampleConfig("ID").toString
if (runConfig.contains("PL")) mapping.RGPL = runConfig("PL").toString
if (runConfig.contains("PU")) mapping.RGPU = runConfig("PU").toString
if (runConfig.contains("CN")) mapping.RGCN = runConfig("CN").toString
mapping.outputDir = runDir
if (startJobs) {
mapping.init
mapping.biopetScript
}
return mapping
}
} }
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