From 9451debea87084117c970ace6eeeb8348cd7bf6a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 9 Mar 2015 09:31:44 +0100
Subject: [PATCH] Added notes
---
.../biopet/pipelines/shiva/ShivaVariantcallingTrait.scala | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
index b29c9efb7..9bc68f233 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
@@ -168,7 +168,9 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
/** Makes a vcf file from a mpileup without statistics */
class RawVcf extends Variantcaller {
val name = "raw"
- protected val defaultPrio = 999
+
+ // This caller is designed as fallback when other variantcallers fails to report
+ protected val defaultPrio = Int.MaxValue
/** Final output file of this mode */
def outputFile = new File(outputDir, namePrefix + ".raw.vcf.gz")
--
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