From e5e47f6c7e9eb78bba7df65185a61e00ae8c996f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 17 Aug 2016 15:33:55 +0200
Subject: [PATCH] Fix default 0
---
.../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 df063a2cd..e7a69b83c 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
@@ -275,8 +275,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
else Map()
}
- 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)")
+ protected val removeOnConflict = Set("Output_file", "Run_time", "Start_time", "End_time", "Novel_/_existing_variants", "Input_file_(format)")
+ protected val nonNumber = Set("VEP_version_(API)", "Cache/Database", "Species", "Command_line_options")
override def resolveSummaryConflict(v1: Any, v2: Any, key: String): Any = {
if (removeOnConflict.contains(key)) None
@@ -303,7 +303,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
val name = header.stripPrefix("[").stripSuffix("]")
name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).map { line =>
val values = line.split("\t", 2)
- values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(0)
+ values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last)
}.toMap)
}).toMap
}
--
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