From c8d00cabafd7594e530431fadb9f333ad2ffaad0 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 17 Mar 2016 12:21:18 +0100
Subject: [PATCH] Simplify file names
---
.../sasc/biopet/pipelines/gwastest/GwasTest.scala | 12 ++++++------
1 file changed, 6 insertions(+), 6 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 55099789f..9e8d529b7 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
@@ -62,21 +62,21 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
val snpTests = BedRecordList.fromReference(referenceFasta())
.scatter(config("bin_size", default = 10^6))
.allRecords.map { region =>
- val bedFile = new File(outputDir, "snptest" + File.separator + region.chr + File.separator +
- s"${region.chr}-${region.start + 1}-${region.end}.bed")
- bedFile.getParentFile.mkdirs()
+ val regionDir = new File(outputDir, "snptest" + File.separator + region.chr)
+ regionDir.mkdirs()
+ val bedFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.bed")
BedRecordList.fromList(List(region)).writeToFile(bedFile)
+ bedFile.deleteOnExit()
val sv = new SelectVariants(this)
sv.inputFiles :+= vcfFile
- sv.outputFile = new File(outputDir, "snptest" + File.separator + region.chr + File.separator +
- s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
+ sv.outputFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
sv.intervals :+= bedFile
sv.isIntermediate = true
add(sv)
//TODO: snptest
- Map()
+ (region -> "")
}
}
}
--
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