From 44654f47fa2a80a764eaa76b9029552e8df75710 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 1 Apr 2016 15:20:45 +0200
Subject: [PATCH] Style changes
---
.../biopet/pipelines/gwastest/GwasTest.scala | 39 ++++++++++---------
1 file changed, 20 insertions(+), 19 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 63fd0ffa8..bfdd64344 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
@@ -66,25 +66,26 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val cvTotal = new CatVariants(this)
cvTotal.assumeSorted = true
cvTotal.outputFile = new File(outputDirGens, "merge.gens.vcf.gz")
- val chrGens = inputGens.groupBy(_.contig).map { case (contig, gens) =>
- val cvChr = new CatVariants(this)
- cvChr.assumeSorted = true
- //cvChr.isIntermediate = true
- cvChr.outputFile = new File(outputDirGens, s"${contig}.merge.gens.vcf.gz")
- gens.zipWithIndex.foreach { gen =>
- val gensToVcf = new GensToVcf(this)
- gensToVcf.inputGens = gen._1.genotypes
- gensToVcf.inputInfo = gen._1.info
- gensToVcf.contig = gen._1.contig
- gensToVcf.samplesFile = phenotypeFile
- gensToVcf.outputVcf = new File(outputDirGens, gen._1.genotypes.getName + s".${gen._2}.vcf.gz")
- gensToVcf.isIntermediate = true
- add(gensToVcf)
- cvChr.inputFiles :+= gensToVcf.outputVcf
- }
- add(cvChr)
- cvTotal.inputFiles :+= cvChr.outputFile
- contig -> cvChr.outputFile
+ val chrGens = inputGens.groupBy(_.contig).map {
+ case (contig, gens) =>
+ val cvChr = new CatVariants(this)
+ cvChr.assumeSorted = true
+ //cvChr.isIntermediate = true
+ cvChr.outputFile = new File(outputDirGens, s"${contig}.merge.gens.vcf.gz")
+ gens.zipWithIndex.foreach { gen =>
+ val gensToVcf = new GensToVcf(this)
+ gensToVcf.inputGens = gen._1.genotypes
+ gensToVcf.inputInfo = gen._1.info
+ gensToVcf.contig = gen._1.contig
+ gensToVcf.samplesFile = phenotypeFile
+ gensToVcf.outputVcf = new File(outputDirGens, gen._1.genotypes.getName + s".${gen._2}.vcf.gz")
+ gensToVcf.isIntermediate = true
+ add(gensToVcf)
+ cvChr.inputFiles :+= gensToVcf.outputVcf
+ }
+ add(cvChr)
+ cvTotal.inputFiles :+= cvChr.outputFile
+ contig -> cvChr.outputFile
}
add(cvTotal)
(cvTotal.outputFile, Map[String, File]())
--
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