From cbd73126850923a40b298d7df68f6ef817c16276 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 16 Aug 2015 15:23:47 +0200
Subject: [PATCH] Added exeption on duplicate sample/libs
---
.../scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
index a461bdcac..f30a45c01 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.core.ToolCommand
import nl.lumc.sasc.biopet.utils.ConfigUtils._
+import scala.collection.mutable
import scala.io.Source
@@ -47,10 +48,15 @@ object SamplesTsvToJson extends ToolCommand {
val libraryColumn = header.indexOf("library")
if (sampleColumn == -1) throw new IllegalStateException("sample column does not exist in: " + inputFile)
+ val sampleLibCache: mutable.Set[(String, Option[String])] = mutable.Set()
+
val librariesValues: List[Map[String, Any]] = for (tsvLine <- lines.tail) yield {
val values = tsvLine.split("\t")
val sample = values(sampleColumn)
val library = if (libraryColumn != -1) Some(values(libraryColumn)) else None
+ if (sampleLibCache.contains((sample, library)))
+ throw new IllegalStateException(s"Combination of $sample and $library is found multiple times")
+ else sampleLibCache.add((sample, library))
val valuesMap = (for (
t <- 0 until values.size if !values(t).isEmpty && t != sampleColumn && t != libraryColumn
) yield header(t) -> values(t)).toMap
--
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