Commit 66a08a19 authored by Peter van 't Hof's avatar Peter van 't Hof

config save check

parent 7be30c47
......@@ -92,10 +92,6 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
} else inputVcf
if (enableScatter) {
val doNotRemove: Boolean = config("do_not_remove", default = false)
if (doNotRemove) {
logger.warn("Chunking combined with do_not_remove possibly leads to mangled CSQ fields")
}
val outputVcfFiles = BedRecordList.fromReference(referenceFasta())
.scatter(config("bin_size", default = 50000000))
.allRecords.map { region =>
......@@ -116,6 +112,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
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)
cv.variant = outputVcfFiles.toList
cv.outputFile = outputVcf
......
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