From e32a9778dcf8c50e914c39976a093c0179afc5dd Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Apr 2016 15:58:20 +0200
Subject: [PATCH] Added error message
---
.../scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
index 53816acdd..10e5eca75 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
@@ -52,7 +52,7 @@ class GensToVcf(val root: Configurable) extends ToolCommandFunction with Referen
override def beforeGraph(): Unit = {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
- if (contig == null) throw new IllegalStateException
+ if (contig == null) throw new IllegalStateException("Contig is missing")
if (outputVcf.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputVcf.getAbsolutePath + ".tbi")
}
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
index fd63c3044..e2f938872 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
@@ -42,7 +42,7 @@ class SnptestToVcf(val root: Configurable) extends ToolCommandFunction with Refe
override def beforeGraph(): Unit = {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
- if (contig == null) Logging.addError("SnptestToVcf is missing a contig")
+ if (contig == null) throw new IllegalStateException("Contig is missing")
//if (outputVcf.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputVcf.getAbsolutePath + ".tbi")
}
--
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