From 944b9af0d38f0484bb63e9c20665ff2fadc7c18d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Feb 2015 11:51:23 +0100
Subject: [PATCH] Added addMultisampleJobs method
---
.../sasc/biopet/core/MultiSampleQScript.scala | 17 ++++++++++++-----
1 file changed, 12 insertions(+), 5 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
index 478a26aa0..0857be0ef 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument }
*/
trait MultiSampleQScript extends BiopetQScript {
@Argument(doc = "Only Sample", shortName = "sample", required = false)
- val onlySample: List[String] = Nil
+ private val onlySamples: List[String] = Nil
require(Config.global.map.contains("samples"), "No Samples found in config")
@@ -94,7 +94,7 @@ trait MultiSampleQScript extends BiopetQScript {
protected def addJobs()
/** function add all libraries in one call */
- protected final def addLibsJobs(): Unit = {
+ protected final def addPerLibJobs(): Unit = {
for ((libraryId, library) <- libraries) {
library.addAndTrackJobs()
}
@@ -128,14 +128,21 @@ trait MultiSampleQScript extends BiopetQScript {
protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
- final def addSamplesJobs() {
- if (onlySample.isEmpty) samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
- else onlySample.foreach(sampleId => samples.get(sampleId) match {
+ final def addPerSampleJobs() {
+ if (onlySamples.isEmpty) {
+ samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
+ addMultiSampleJobs()
+ } else onlySamples.foreach(sampleId => samples.get(sampleId) match {
case Some(sample) => sample.addAndTrackJobs()
case None => logger.warn("sampleId '" + sampleId + "' not found")
})
}
+ /**
+ * Method where the multisample jobs should be added, this will be executed only when running the -sample argument is not given
+ */
+ def addMultiSampleJobs()
+
/** Stores sample state */
private var currentSample: Option[String] = None
--
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