From a081627f46f16fe010a680187f2a394fa4e4502c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Apr 2016 08:42:38 +0200
Subject: [PATCH] Fixed defaults
---
.../main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala | 6 +++---
.../nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala | 4 ++--
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
index fc7f13aae..1bd138070 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
@@ -58,7 +58,7 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
var sexColumn: Option[String] = config("sex_column")
var stratifyOn: Option[String] = config("stratify_on")
- var conditionOn: List[String] = config("condition_on")
+ var conditionOn: List[String] = config("condition_on", default = Nil)
var priorAdd: List[String] = config("prior_add", default = Nil)
var priorCov: List[String] = config("prior_cov", default = Nil)
@@ -90,8 +90,8 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
var range: List[String] = config("range", default = Nil)
var renorm: Boolean = config("renorm", default = false)
var snpid: List[String] = config("snpid", default = Nil)
- var useRawCovariates: Boolean = config("use_raw_covariates")
- var useRawPhenotypes: Boolean = config("use_raw_phenotypes")
+ var useRawCovariates: Boolean = config("use_raw_covariates", default = false)
+ var useRawPhenotypes: Boolean = config("use_raw_phenotypes", default = false)
var noClobber: Boolean = config("no_clobber", default = false)
executable = config("exe", default = "snptest")
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
index a64a373f5..440dbb5c5 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/SnptestToVcf.scala
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
-import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
*
--
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