From 8a6f4376830a46609941f8f6c4e368461f0dee8d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 14 Mar 2016 16:07:55 +0100
Subject: [PATCH] Fix free vars
---
.../sasc/biopet/extensions/Freebayes.scala | 22 +++++++++----------
1 file changed, 11 insertions(+), 11 deletions(-)
diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
index b70070413..e61b4c1c1 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Freebayes.scala
@@ -41,22 +41,22 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var bamList: Option[File] = config("bam_list")
@Input(required = false)
- var targets: Option[File] = config("targets")
+ var targets: Option[File] = config("targets", freeVar = false)
@Input(required = false)
- var samples: Option[File] = config("samples")
+ var samples: Option[File] = config("samples", freeVar = false)
@Input(required = false)
- var populations: Option[File] = config("populations")
+ var populations: Option[File] = config("populations", freeVar = false)
@Input(required = false)
- var cnvMap: Option[File] = config("cnv_map")
+ var cnvMap: Option[File] = config("cnv_map", freeVar = false)
@Input(required = false)
- var trace: Option[File] = config("trace")
+ var trace: Option[File] = config("trace", freeVar = false)
@Input(required = false)
- var failedAlleles: Option[File] = config("failed_alleles")
+ var failedAlleles: Option[File] = config("failed_alleles", freeVar = false)
@Input(required = false)
var observationBias: Option[File] = config("observation_bias")
@@ -65,14 +65,14 @@ class Freebayes(val root: Configurable) extends BiopetCommandLineFunction with R
var contaminationEstimates: Option[File] = config("contamination_estimates")
@Input(required = false)
- var variantInput: Option[File] = config("variant_input")
+ var variantInput: Option[File] = config("variant_input", freeVar = false)
@Input(required = false)
- var haplotypeBasisAlleles: Option[File] = config("haplotype_basis_alleles")
+ var haplotypeBasisAlleles: Option[File] = config("haplotype_basis_alleles", freeVar = false)
- var pvar: Option[Int] = config("pvar")
- var theta: Option[Int] = config("theta")
- var ploidy: Option[Int] = config("ploidy")
+ var pvar: Option[Int] = config("pvar", freeVar = false)
+ var theta: Option[Int] = config("theta", freeVar = false)
+ var ploidy: Option[Int] = config("ploidy", freeVar = false)
var useBestNAlleles: Option[Int] = config("use_best_n_alleles")
var maxComplexGap: Option[Int] = config("max_complex_gap")
var minRepeatSize: Option[Int] = config("min_repeat_size")
--
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