From e7667c93628213d375965dbbfb2cddba66b594e5 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 13 May 2016 15:06:58 +0200
Subject: [PATCH] Added java match
---
.../sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala | 1 +
1 file changed, 1 insertion(+)
diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
index 0f59d8776..a2c02fa8f 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/GenerateIndexes.scala
@@ -63,6 +63,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
val fastaUris = genomeConfig.getOrElse("fasta_uri",
throw new IllegalArgumentException(s"No fasta_uri found for $speciesName - $genomeName")) match {
case a: Traversable[_] => a.map(_.toString).toArray
+ case a: util.ArrayList[_] => a.map(_.toString).toArray
case a => Array(a.toString)
}
--
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