Commit b7b1a0f3 authored by Sander Bollen's avatar Sander Bollen
Browse files

there's a bug in VEP:

the `failed` flag should be a flag per the documentation
(see:
 http://grch37.ensembl.org/info/docs/tools/vep/script/vep_options.html,
and
http://oct2014.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html )
But, when running, it requires a numeric value.
When running the VEP with verbose mode, it
appears that all boolean flags get converted to 1.
Therefore, I'm setting `failed` to have value 1.
parent 369147f4
...@@ -75,7 +75,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu ...@@ -75,7 +75,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var maf_esp: Boolean = config("maf_esp", default = false) var maf_esp: Boolean = config("maf_esp", default = false)
var old_map: Boolean = config("old_maf", default = false) var old_map: Boolean = config("old_maf", default = false)
var pubmed: Boolean = config("pubmed", default = false) var pubmed: Boolean = config("pubmed", default = false)
var failed: Boolean = config("failed", default = false)
var vcf: Boolean = config("vcf", default = true) var vcf: Boolean = config("vcf", default = true)
var json: Boolean = config("json", default = false) var json: Boolean = config("json", default = false)
var gvf: Boolean = config("gvf", default = false) var gvf: Boolean = config("gvf", default = false)
...@@ -140,6 +140,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu ...@@ -140,6 +140,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var port: Option[Int] = config("port") var port: Option[Int] = config("port")
var db_version: Option[Int] = config("db_version") var db_version: Option[Int] = config("db_version")
var buffer_size: Option[Int] = config("buffer_size") var buffer_size: Option[Int] = config("buffer_size")
// ought to be a flag, but is BUG in VEP; becomes numeric ("1" is true)
var failed: Option[Int] = config("failed")
override def beforeGraph(): Unit = { override def beforeGraph(): Unit = {
super.beforeGraph() super.beforeGraph()
...@@ -189,7 +191,6 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu ...@@ -189,7 +191,6 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
conditional(maf_1kg, "--maf_1kg") + conditional(maf_1kg, "--maf_1kg") +
conditional(maf_esp, "--maf_esp") + conditional(maf_esp, "--maf_esp") +
conditional(pubmed, "--pubmed") + conditional(pubmed, "--pubmed") +
conditional(failed, "--failed") +
conditional(vcf, "--vcf") + conditional(vcf, "--vcf") +
conditional(json, "--json") + conditional(json, "--json") +
conditional(gvf, "--gvf") + conditional(gvf, "--gvf") +
...@@ -249,6 +250,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu ...@@ -249,6 +250,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
optional("--freq_freq", freq_freq) + optional("--freq_freq", freq_freq) +
optional("--port", port) + optional("--port", port) +
optional("--db_version", db_version) + optional("--db_version", db_version) +
optional("--buffer_size", buffer_size) optional("--buffer_size", buffer_size) +
optional("--failed", failed)
} }
...@@ -39,7 +39,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum ...@@ -39,7 +39,7 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
} }
override def defaults = Map( override def defaults = Map(
"varianteffectpredictor" -> Map("everything" -> true, "failed" -> true) "varianteffectpredictor" -> Map("everything" -> true, "failed" -> 1, "allow_non_variant" -> true)
) )
//defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true)) //defaults ++= Map("varianteffectpredictor" -> Map("everything" -> true))
......
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