From 6645955ea453995d8348364f507b33eba612711e Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 16 Aug 2015 15:11:04 +0200
Subject: [PATCH] Switched library to an Option[String]
---
.../nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala | 10 ++++------
1 file changed, 4 insertions(+), 6 deletions(-)
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 46cd2b40c..a461bdcac 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
@@ -50,16 +50,14 @@ object SamplesTsvToJson extends ToolCommand {
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) values(libraryColumn) else null
+ val library = if (libraryColumn != -1) Some(values(libraryColumn)) else None
val valuesMap = (for (
t <- 0 until values.size if !values(t).isEmpty && t != sampleColumn && t != libraryColumn
) yield header(t) -> values(t)).toMap
- val map: Map[String, Any] = if (library != null) {
- Map("samples" -> Map(sample -> Map("libraries" -> Map(library -> valuesMap))))
- } else {
- Map("samples" -> Map(sample -> valuesMap))
+ library match {
+ case Some(lib) => Map("samples" -> Map(sample -> Map("libraries" -> Map(library -> valuesMap))))
+ case _ => Map("samples" -> Map(sample -> valuesMap))
}
- map
}
librariesValues.foldLeft(Map[String, Any]())((acc, kv) => mergeMaps(acc, kv))
}
--
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