Commit cfeefcd4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix code warnings

parent 13825363
......@@ -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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