From a49982eff2be61a935f4704b4144c0f150183c72 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 8 Apr 2016 10:41:13 +0200
Subject: [PATCH] Switch to other dir for bed files
---
.../nl/lumc/sasc/biopet/tools/SnptestToVcf.scala | 4 ++--
.../sasc/biopet/pipelines/gwastest/GwasTest.scala | 12 +++++++-----
2 files changed, 9 insertions(+), 7 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 f990a0e4d..19bc0c112 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
@@ -60,11 +60,11 @@ object SnptestToVcf extends ToolCommand {
val reference = new FastaSequenceFile(referenceFasta, true)
val vcfHeader = new VCFHeader()
vcfHeader.setSequenceDictionary(reference.getSequenceDictionary)
- val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder()
+ val writer = new VariantContextWriterBuilder()
.setOutputFile(outputVcf)
.setReferenceDictionary(vcfHeader.getSequenceDictionary)
.unsetOption(Options.INDEX_ON_THE_FLY)
- .build)
+ .build
writer.writeHeader(vcfHeader)
writer.close()
}
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 ce4d48ef4..69539ec40 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
@@ -94,15 +94,17 @@ 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 regionDir = new File(outputDir, "snptest" + File.separator + region.chr)
+ val name = s"${region.chr}-${region.start + 1}-${region.end}"
+
+ val regionDir = new File(outputDir, ".queue" + File.separator + "regions" + File.separator + region.chr)
regionDir.mkdirs()
- val bedFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.bed")
+ val bedFile = new File(regionDir, s"${name}.bed")
BedRecordList.fromList(List(region)).writeToFile(bedFile)
bedFile.deleteOnExit()
val sv = new SelectVariants(this)
sv.inputFiles :+= chrVcfFiles.getOrElse(region.chr, vcfFile)
- sv.outputFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
+ sv.outputFile = new File(regionDir, s"${name}.vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
add(sv)
@@ -110,12 +112,12 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val snptest = new Snptest(this)
snptest.inputGenotypes :+= sv.outputFile
snptest.inputSampleFiles :+= phenotypeFile
- snptest.outputFile = Some(new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.snptest"))
+ snptest.outputFile = Some(new File(regionDir, s"${name}.snptest"))
add(snptest)
val snptestToVcf = new SnptestToVcf(this)
snptestToVcf.inputInfo = snptest.outputFile.get
- snptestToVcf.outputVcf = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.snptest.vcf.gz")
+ snptestToVcf.outputVcf = new File(regionDir, s"${name}.snptest.vcf.gz")
snptestToVcf.contig = region.chr
add(snptestToVcf)
--
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