Commit b7b1a0f3 authored by Sander Bollen's avatar Sander Bollen

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
var maf_esp: Boolean = config("maf_esp", default = false)
var old_map: Boolean = config("old_maf", default = false)
var pubmed: Boolean = config("pubmed", default = false)
var failed: Boolean = config("failed", default = false)
var vcf: Boolean = config("vcf", default = true)
var json: Boolean = config("json", default = false)
var gvf: Boolean = config("gvf", default = false)
......@@ -140,6 +140,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var port: Option[Int] = config("port")
var db_version: Option[Int] = config("db_version")
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 = {
super.beforeGraph()
......@@ -189,7 +191,6 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
conditional(maf_1kg, "--maf_1kg") +
conditional(maf_esp, "--maf_esp") +
conditional(pubmed, "--pubmed") +
conditional(failed, "--failed") +
conditional(vcf, "--vcf") +
conditional(json, "--json") +
conditional(gvf, "--gvf") +
......@@ -249,6 +250,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
optional("--freq_freq", freq_freq) +
optional("--port", port) +
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
}
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))
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment