From d891d46f83b89797f037d6be993db6a587bb1a10 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 21 Mar 2016 18:33:37 +0100
Subject: [PATCH] Fixed scattering
---
.../biopet/pipelines/gwastest/GwasTest.scala | 28 ++++++++-----------
1 file changed, 12 insertions(+), 16 deletions(-)
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 25d79452d..9c659718e 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()
--
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