Commit 2b62b86b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Rename function

parent 66bebf8a
...@@ -28,10 +28,10 @@ trait MultiSampleQScript extends BiopetQScript { ...@@ -28,10 +28,10 @@ trait MultiSampleQScript extends BiopetQScript {
if (!Config.global.map.contains("samples")) logger.warn("No Samples found in config") if (!Config.global.map.contains("samples")) logger.warn("No Samples found in config")
abstract class AbstractSample(val sampleId: String) { abstract class AbstractSample(val sampleId: String) {
val config = new ConfigFunctions(defaultSample = Some(sampleId)) val config = new ConfigFunctions(defaultSample = sampleId)
abstract class AbstractLibrary(val libraryId: String) { abstract class AbstractLibrary(val libraryId: String) {
val config = new ConfigFunctions(defaultSample = Some(sampleId), defaultLibrary = Some(libraryId)) val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libraryId)
final def run(): Unit = { final def run(): Unit = {
currentSample = Some(sampleId) currentSample = Some(sampleId)
currentLibrary = Some(libraryId) currentLibrary = Some(libraryId)
...@@ -41,7 +41,7 @@ trait MultiSampleQScript extends BiopetQScript { ...@@ -41,7 +41,7 @@ trait MultiSampleQScript extends BiopetQScript {
} }
def getLibraryDir: String = { def getLibraryDir: String = {
getSampleDir + "libraries" + File.pathSeparator + libraryId + File.pathSeparator getSampleDir + "lib_" + libraryId + File.separator
} }
protected def runJobs() protected def runJobs()
...@@ -49,9 +49,9 @@ trait MultiSampleQScript extends BiopetQScript { ...@@ -49,9 +49,9 @@ trait MultiSampleQScript extends BiopetQScript {
type Library <: AbstractLibrary type Library <: AbstractLibrary
val libraries: Map[String, Library] = getLibrariesIds.map(id => id -> initLibrary(id)).toMap val libraries: Map[String, Library] = getLibrariesIds.map(id => id -> makeLibrary(id)).toMap
def initLibrary(id: String): Library def makeLibrary(id: String): Library
protected def getLibrariesIds: Set[String] = { protected def getLibrariesIds: Set[String] = {
ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet ConfigUtils.getMapFromPath(Config.global.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
...@@ -78,9 +78,9 @@ trait MultiSampleQScript extends BiopetQScript { ...@@ -78,9 +78,9 @@ trait MultiSampleQScript extends BiopetQScript {
type Sample <: AbstractSample type Sample <: AbstractSample
def initSample(id: String): Sample def makeSample(id: String): Sample
val samples: Map[String, Sample] = getSamplesIds.map(id => id -> initSample(id)).toMap val samples: Map[String, Sample] = getSamplesIds.map(id => id -> makeSample(id)).toMap
/** Returns a list of all sampleIDs */ /** Returns a list of all sampleIDs */
protected def getSamplesIds: Set[String] = if (onlySample != Nil) onlySample.toSet else { protected def getSamplesIds: Set[String] = if (onlySample != Nil) onlySample.toSet else {
......
...@@ -22,10 +22,10 @@ import org.broadinstitute.gatk.queue.QScript ...@@ -22,10 +22,10 @@ import org.broadinstitute.gatk.queue.QScript
class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript { class MultisamplePipelineTemplate(val root: Configurable) extends QScript with MultiSampleQScript {
def this() = this(null) def this() = this(null)
def initSample(id: String) = new Sample(id) def makeSample(id: String) = new Sample(id)
class Sample(sampleId: String) extends AbstractSample(sampleId) { class Sample(sampleId: String) extends AbstractSample(sampleId) {
def initLibrary(id: String) = new Library(id) def makeLibrary(id: String) = new Library(id)
class Library(libraryId: String) extends AbstractLibrary(libraryId) { class Library(libraryId: String) extends AbstractLibrary(libraryId) {
def runJobs(): Unit = { def runJobs(): Unit = {
// Library jobs // Library jobs
......
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