From 77d657ac0a6206866a2a6e7e9b184508e0f9e333 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 17 Aug 2016 16:50:51 +0200
Subject: [PATCH] Skip empty values
---
.../lumc/sasc/biopet/extensions/VariantEffectPredictor.scala | 5 +++--
1 file changed, 3 insertions(+), 2 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 e7a69b83c..087e4ceca 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
@@ -301,9 +301,10 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
(for ((header, headerIndex) <- headers) yield {
val name = header.stripPrefix("[").stripSuffix("]")
- name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).map { line =>
+ name.replaceAll(" ", "_") -> (contents.drop(headerIndex + 1).takeWhile(!isHeader(_)).flatMap { line =>
val values = line.split("\t", 2)
- values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last)
+ if (values.last.isEmpty || values.last == "-") None
+ else Some(values.head.replaceAll(" ", "_") -> tryToParseNumber(values.last).getOrElse(values.last))
}.toMap)
}).toMap
}
--
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