From fcecdf0c223ee52de6b2d28e48d5d6e5498155b7 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 5 Aug 2016 15:37:21 +0200
Subject: [PATCH] Change key sets
---
.../sasc/biopet/extensions/VariantEffectPredictor.scala | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
index cb231e7b3..df063a2cd 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
@@ -275,12 +275,12 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
else Map()
}
- protected val removeOnConflict = Set("Output_file", "Command_line_options", "Run_time", "Start_time", "End_time", "Input_file_(format)", "Novel_/_existing_variants")
- protected val nonNumber = Set("VEP_version_(API)", "Cache/Database", "Species")
+ protected val removeOnConflict = Set("Output_file", "Run_time", "Start_time", "End_time", "Novel_/_existing_variants")
+ protected val nonNumber = Set("VEP_version_(API)", "Cache/Database", "Species", "Command_line_options", "Input_file_(format)")
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
if (removeOnConflict.contains(key)) None
- else if (nonNumber.contains(key)) v1
+ else if (nonNumber.contains(key)) v2
else {
(v1, v2) match {
case (x1: Int, x2: Int) => x1 + x2
--
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