From 1f17e7c637c05e036d0f89193ce919ab2b719f8a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sat, 14 May 2016 17:42:44 +0200
Subject: [PATCH] Improved message
---
.../nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala | 4 ++--
.../scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala | 2 +-
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
index 7ea77993b..6a56118e2 100644
--- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
@@ -73,8 +73,8 @@ class BamMetrics(val root: Configurable) extends QScript
/** executed before script */
def init(): Unit = {
inputFiles :+= new InputFile(inputBam)
- ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta()))
- roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta()))
+ ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
+ roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
}
/** Script to add jobs */
diff --git a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala
index 081ea5bd3..7cbee938b 100644
--- a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala
+++ b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedCheck.scala
@@ -19,7 +19,7 @@ object BedCheck {
try {
bedrecords.validateContigs(reference)
} catch {
- case e: IllegalArgumentException => Logging.addError(e.getMessage)
+ case e: IllegalArgumentException => Logging.addError(e.getMessage + s", Bedfile: $bedFile")
}
} else bedrecords.validateContigs(reference)
}
--
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