Commit 2c1fb614 authored by Sander Bollen's avatar Sander Bollen

Warning message for #385

parent 6efe0956
......@@ -58,9 +58,9 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
lazy val enableScatter: Boolean = config("enable_scatter", default = {
val ref = new FastaSequenceFile(referenceFasta(), true)
val refLenght = ref.getSequenceDictionary.getReferenceLength
val refLength = ref.getSequenceDictionary.getReferenceLength
ref.close()
refLenght > minScatterGenomeSize
refLength > minScatterGenomeSize
})
def sampleInfo: Map[String, Map[String, Any]] = root match {
......@@ -92,6 +92,10 @@ class Toucan(val root: Configurable) extends QScript with BiopetQScript with Sum
} else inputVcf
if (enableScatter) {
val doNotRemove: Boolean = config("do_not_remove", namespace = "variant_effect_predictor", 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 =>
......
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