From ebe731f3de402d310c5edb940b525f3a3808a355 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 3 Feb 2015 10:06:21 +0100
Subject: [PATCH] Fix for -sample commandline argument
---
.../lumc/sasc/biopet/core/MultiSampleQScript.scala | 12 ++++++------
1 file changed, 6 insertions(+), 6 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 67f108b3a..478a26aa0 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
@@ -125,15 +125,15 @@ trait MultiSampleQScript extends BiopetQScript {
val samples: Map[String, Sample] = sampleIds.map(id => id -> makeSample(id)).toMap
/** Returns a list of all sampleIDs */
- protected def sampleIds: Set[String] = if (onlySample != Nil) onlySample.toSet else {
- ConfigUtils.any2map(Config.global.map("samples")).keySet
- }
+ protected def sampleIds: Set[String] = ConfigUtils.any2map(Config.global.map("samples")).keySet
/** Runs addAndTrackJobs method for each sample */
final def addSamplesJobs() {
- for ((sampleId, sample) <- samples) {
- sample.addAndTrackJobs()
- }
+ if (onlySample.isEmpty) samples.foreach { case (sampleId, sample) => sample.addAndTrackJobs() }
+ else onlySample.foreach(sampleId => samples.get(sampleId) match {
+ case Some(sample) => sample.addAndTrackJobs()
+ case None => logger.warn("sampleId '" + sampleId + "' not found")
+ })
}
/** Stores sample state */
--
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