From 53c4ba81f32f3a5bf1aac582a4d4cafb58f1eaea Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 27 Feb 2015 16:50:47 +0100
Subject: [PATCH] Add default function to add summarizable
---
.../sasc/biopet/core/MultiSampleQScript.scala | 22 +++++++++++++++++--
1 file changed, 20 insertions(+), 2 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 c153011bb..c3713be10 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
@@ -49,12 +49,21 @@ trait MultiSampleQScript extends SummaryQScript {
/** Overrules config of qscript with default sample and default library */
val config = new ConfigFunctions(defaultSample = sampleId, defaultLibrary = libId)
+ /**
+ * Name overules the one from qscript
+ * @param summarizable
+ * @param name
+ */
+ def addSummarizable(summarizable: Summarizable, name: String): Unit = {
+ qscript.addSummarizable(summarizable, name, Some(sampleId), Some(libId))
+ }
+
/** Adds the library jobs */
final def addAndTrackJobs(): Unit = {
currentSample = Some(sampleId)
currentLib = Some(libId)
addJobs()
- addSummarizable(this, "pipeline", Some(sampleId), Some(libId))
+ qscript.addSummarizable(this, "pipeline", Some(sampleId), Some(libId))
currentLib = None
currentSample = None
}
@@ -87,11 +96,20 @@ trait MultiSampleQScript extends SummaryQScript {
ConfigUtils.getMapFromPath(globalConfig.map, List("samples", sampleId, "libraries")).getOrElse(Map()).keySet
}
+ /**
+ * Name overules the one from qscript
+ * @param summarizable
+ * @param name
+ */
+ def addSummarizable(summarizable: Summarizable, name: String): Unit = {
+ qscript.addSummarizable(summarizable, name, Some(sampleId))
+ }
+
/** Adds sample jobs */
final def addAndTrackJobs(): Unit = {
currentSample = Some(sampleId)
addJobs()
- addSummarizable(this, "pipeline", Some(sampleId))
+ qscript.addSummarizable(this, "pipeline", Some(sampleId))
currentSample = None
}
--
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