From 7852e631225d009ce0659015c658687b05f4f0ee Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 13 Apr 2015 14:01:40 +0200
Subject: [PATCH] Fixed parsing of empty values
---
.../scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
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 6058a5fc4..bf3955b5e 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
@@ -53,7 +53,8 @@ object SamplesTsvToJson extends ToolCommand {
val values = tsvLine.split("\t")
val sample = values(sampleColumn)
val library = if (libraryColumn != -1) values(libraryColumn) else null
- val valuesMap = (for (t <- 0 until values.size if t != sampleColumn if t != libraryColumn) yield (header(t) -> values(t))).toMap
+ 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 {
--
GitLab