From 72bc5c67eb5e97923a5add0d429ab1f44159bda4 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Apr 2016 11:10:23 +0200
Subject: [PATCH] Format
---
.../main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala | 2 +-
.../nl/lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
index 19bc0c112..2473c7bfe 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SnptestToVcf.scala
@@ -48,7 +48,7 @@ object SnptestToVcf extends ToolCommand {
infoHeader match {
case Some(header) => parseLines(header, infoIt, cmdArgs)
- case _ =>
+ case _ =>
writeEmptyVcf(cmdArgs.outputVcf, cmdArgs.referenceFasta)
logger.info("No header and records found in file")
}
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 69539ec40..117cf84f0 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
@@ -94,9 +94,9 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val snpTests = BedRecordList.fromReference(referenceFasta())
.scatter(config("bin_size", default = 1000000))
.allRecords.map { region =>
- val name = s"${region.chr}-${region.start + 1}-${region.end}"
+ val name = s"${region.chr}-${region.start + 1}-${region.end}"
- val regionDir = new File(outputDir, ".queue" + File.separator + "regions" + File.separator + region.chr)
+ val regionDir = new File(outputDir, ".queue" + File.separator + "regions" + File.separator + region.chr)
regionDir.mkdirs()
val bedFile = new File(regionDir, s"${name}.bed")
BedRecordList.fromList(List(region)).writeToFile(bedFile)
--
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