From 3fb6b5f89825542bfa62c0e96cdf240ca1db9b66 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 19 Jan 2016 13:19:31 +0100
Subject: [PATCH] Fixed error message in bamutils
---
.../src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
index f13230534..d0c185cf1 100644
--- a/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
+++ b/public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala
@@ -25,7 +25,8 @@ object BamUtils {
val inputSam = SamReaderFactory.makeDefault.open(file)
val samples = inputSam.getFileHeader.getReadGroups.map(_.getSample).distinct
if (samples.size == 1) samples.head -> file
- else throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
+ else if (samples.size > 1) throw new IllegalArgumentException("Bam contains multiple sample IDs: " + file)
+ else throw new IllegalArgumentException("Bam does not contain sample ID or have no readgroups defined: " + file)
}
if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice")
temp.toMap
--
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