From 4997527823a76f60385d923768e61d996cd612ca Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Thu, 17 Mar 2016 11:24:07 +0100
Subject: [PATCH] Add scatter
---
.../lumc/sasc/biopet/pipelines/gwastest/GwasTest.scala | 10 +++++++++-
1 file changed, 9 insertions(+), 1 deletion(-)
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 17f2dca19..58a445ac0 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
@@ -4,6 +4,7 @@ import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, BiopetQScript}
import nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import nl.lumc.sasc.biopet.extensions.tools.GensToVcf
import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
import org.broadinstitute.gatk.queue.QScript
/**
@@ -55,7 +56,14 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
cv.outputFile
}
- //TODO: snptest
+ val snpTests = BedRecordList.fromReference(referenceFasta())
+ .scatter(config("bin_size", default = 10^6))
+ .allRecords.map { region =>
+ //TODO: bcftools view
+
+ //TODO: snptest
+ Map()
+ }
}
}
--
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