From 21f352a2a8a41b844dfb3038198c008844ff9cad Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 1 Apr 2016 14:54:57 +0200
Subject: [PATCH] Added contig based merge step
---
.../biopet/pipelines/gwastest/GwasTest.scala | 43 +++++++++++--------
1 file changed, 26 insertions(+), 17 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 bb46c08c6..63fd0ffa8 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
@@ -60,25 +60,34 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
/** Pipeline itself */
def biopetScript(): Unit = {
- val vcfFile: File = inputVcf.getOrElse {
+ val (vcfFile, chrVcfFiles): (File, Map[String, File]) = inputVcf.map((_, Map[String, File]())).getOrElse {
require(inputGens.nonEmpty, "No vcf file or gens files defined in config")
val outputDirGens = new File(outputDir, "gens_to_vcf")
- val cv = new CatVariants(this)
- cv.assumeSorted = true
- cv.outputFile = new File(outputDirGens, "merge.gens.vcf.gz")
- inputGens.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".${gen._2}.vcf.gz")
- gensToVcf.isIntermediate = true
- add(gensToVcf)
- cv.inputFiles :+= gensToVcf.outputVcf
+ val cvTotal = new CatVariants(this)
+ cvTotal.assumeSorted = true
+ cvTotal.outputFile = new File(outputDirGens, "merge.gens.vcf.gz")
+ val chrGens = inputGens.groupBy(_.contig).map { case (contig, gens) =>
+ val cvChr = new CatVariants(this)
+ cvChr.assumeSorted = true
+ //cvChr.isIntermediate = true
+ cvChr.outputFile = new File(outputDirGens, s"${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".${gen._2}.vcf.gz")
+ gensToVcf.isIntermediate = true
+ add(gensToVcf)
+ cvChr.inputFiles :+= gensToVcf.outputVcf
+ }
+ add(cvChr)
+ cvTotal.inputFiles :+= cvChr.outputFile
+ contig -> cvChr.outputFile
}
- add(cv)
- cv.outputFile
+ add(cvTotal)
+ (cvTotal.outputFile, Map[String, File]())
}
val snpTests = BedRecordList.fromReference(referenceFasta())
@@ -91,7 +100,7 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
bedFile.deleteOnExit()
val sv = new SelectVariants(this)
- sv.inputFiles :+= vcfFile
+ sv.inputFiles :+= chrVcfFiles.getOrElse(region.chr, vcfFile)
sv.outputFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
--
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