From cfeefcd46ab388a0195475757f88a6b875123a3d Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 11 Apr 2016 08:06:40 +0200
Subject: [PATCH] Fix code warnings
---
.../sasc/biopet/pipelines/gwastest/GwasTest.scala | 14 +++++++-------
1 file changed, 7 insertions(+), 7 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 d65b658f3..29fe44ec0 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
@@ -31,7 +31,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val specsFile: Option[File] = config("imute_specs_file")
val inputGens: List[GensInput] = if (inputVcf.isDefined) List[GensInput]()
- else config("input_gens", default = Nil).asList.map(x => x match {
+ else config("input_gens", default = Nil).asList.map {
case value: Map[String, Any] =>
GensInput(new File(value("genotypes").toString),
value.get("info").map(x => new File(x.toString)),
@@ -41,7 +41,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
value.toMap.get("info").map(x => new File(x.toString)),
value.get("contig").toString)
case _ => throw new IllegalArgumentException
- }) ++ (specsFile match {
+ } ++ (specsFile match {
case Some(file) => imputeSpecsToGensInput(file, config("validate_specs", default = true))
case _ => Nil
})
@@ -73,7 +73,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val cvChr = new CatVariants(this)
cvChr.assumeSorted = true
//cvChr.isIntermediate = true
- cvChr.outputFile = new File(outputDirGens, s"${contig}.merge.gens.vcf.gz")
+ cvChr.outputFile = new File(outputDirGens, s"$contig.merge.gens.vcf.gz")
gens.zipWithIndex.foreach { gen =>
val gensToVcf = new GensToVcf(this)
gensToVcf.inputGens = gen._1.genotypes
@@ -101,13 +101,13 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val regionDir = new File(outputDir, "snptest" + File.separator + region.chr)
val bedDir = new File(outputDir, ".queue" + File.separator + "regions" + File.separator + region.chr)
bedDir.mkdirs()
- val bedFile = new File(bedDir, s"${name}.bed")
+ val bedFile = new File(bedDir, s"$name.bed")
BedRecordList.fromList(List(region)).writeToFile(bedFile)
bedFile.deleteOnExit()
val sv = new SelectVariants(this)
sv.inputFiles :+= chrVcfFiles.getOrElse(region.chr, vcfFile)
- sv.outputFile = new File(regionDir, s"${name}.vcf.gz")
+ sv.outputFile = new File(regionDir, s"$name.vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
add(sv)
@@ -115,12 +115,12 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val snptest = new Snptest(this)
snptest.inputGenotypes :+= sv.outputFile
snptest.inputSampleFiles :+= phenotypeFile
- snptest.outputFile = Some(new File(regionDir, s"${name}.snptest"))
+ snptest.outputFile = Some(new File(regionDir, s"$name.snptest"))
add(snptest)
val snptestToVcf = new SnptestToVcf(this)
snptestToVcf.inputInfo = snptest.outputFile.get
- snptestToVcf.outputVcf = new File(regionDir, s"${name}.snptest.vcf.gz")
+ snptestToVcf.outputVcf = new File(regionDir, s"$name.snptest.vcf.gz")
snptestToVcf.contig = region.chr
add(snptestToVcf)
--
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