Commit d43c8265 authored by Peter van 't Hof's avatar Peter van 't Hof

Merge branch 'warning-do-note-remove' into 'develop'

Warning do note remove



See merge request !453
parents 8a710c02 66a08a19
...@@ -58,9 +58,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum ...@@ -58,9 +58,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
lazy val enableScatter: Boolean = config("enable_scatter", default = { lazy val enableScatter: Boolean = config("enable_scatter", default = {
val ref = new FastaSequenceFile(referenceFasta(), true) val ref = new FastaSequenceFile(referenceFasta(), true)
val refLenght = ref.getSequenceDictionary.getReferenceLength val refLength = ref.getSequenceDictionary.getReferenceLength
ref.close() ref.close()
refLenght > minScatterGenomeSize refLength > minScatterGenomeSize
}) })
def sampleInfo: Map[String, Map[String, Any]] = root match { def sampleInfo: Map[String, Map[String, Any]] = root match {
...@@ -112,6 +112,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum ...@@ -112,6 +112,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
runChunk(sv.out, chunkDir, chunkName) runChunk(sv.out, chunkDir, chunkName)
} }
if (this.functions.filter(_.isInstanceOf[VepNormalizer]).exists(_.asInstanceOf[VepNormalizer].doNotRemove))
logger.warn("Chunking combined with do_not_remove possibly leads to mangled CSQ fields")
val cv = new CatVariants(this) val cv = new CatVariants(this)
cv.variant = outputVcfFiles.toList cv.variant = outputVcfFiles.toList
cv.outputFile = outputVcf cv.outputFile = outputVcf
......
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