diff --git a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala index 25d79452d4719988f7a89589d6e75196fe6f3b11..9c659718e668a13b1bff9f99a670ac097baf59c9 100644 --- a/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala +++ b/public/gwas-test/src/main/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala @@ -25,21 +25,17 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R case class GensInput(genotypes: File, info: Option[File], contig: String) val inputBlaGens: List[GensInput] = if (inputVcf.isDefined) List[GensInput]() - else { - println("blabla") - config("input_gens", default = Nil).asList.map(x => x match { - case value: Map[String, Any] => - GensInput(new File(value("genotypes").toString), - value.get("info").map(x => new File(x.toString)), - value("contig").toString) - case value: util.LinkedHashMap[_, _] => - GensInput(new File(value("genotypes").toString), - value.toMap.get("info").map(x => new File(x.toString)), - value("contig").toString) - case _ => throw new IllegalArgumentException - }) - List[GensInput]() - } + else config("input_gens", default = Nil).asList.map(x => x match { + case value: Map[String, Any] => + GensInput(new File(value("genotypes").toString), + value.get("info").map(x => new File(x.toString)), + value("contig").toString) + case value: util.LinkedHashMap[String, _] => + GensInput(new File(value.get("genotypes").toString), + value.toMap.get("info").map(x => new File(x.toString)), + value.get("contig").toString) + case _ => throw new IllegalArgumentException + }) /** Init for pipeline */ def init(): Unit = { @@ -69,7 +65,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R } val snpTests = BedRecordList.fromReference(referenceFasta()) - .scatter(config("bin_size", default = 10 ^ 6)) + .scatter(config("bin_size", default = 1000000)) .allRecords.map { region => val regionDir = new File(outputDir, "snptest" + File.separator + region.chr) regionDir.mkdirs()