diff --git a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
index 1308a836f667d64503f3788fe2c131a8db10dddd..65abc60985a05edcd07aee8646f5b0c04ca839ed 100644
--- a/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
+++ b/public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import java.io.File
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
* Extension for CombineVariants from GATK
diff --git a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
index b94d24ac7dae43449bebd1a8c04a76a556f7f240..4cb4548a0997d3dd8ddb0189718ec5be294b82b2 100644
--- a/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
+++ b/public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/GensToVcf.scala
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.extensions.tools
import java.io.File
-import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
import nl.lumc.sasc.biopet.utils.Logging
import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
/**
*
diff --git a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
index 18657c0863892428b77920b56b0aa8464d774a7d..6b989655a6636a07c51d1f08d331183e988fbbbb 100644
--- a/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
+++ b/public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala
@@ -14,8 +14,8 @@ import scala.collection.JavaConversions._
import scala.io.Source
/**
- * Created by pjvanthof on 15/03/16.
- */
+ * Created by pjvanthof on 15/03/16.
+ */
object GensToVcf extends ToolCommand {
case class Args(inputGenotypes: File = null,
@@ -79,23 +79,24 @@ object GensToVcf extends ToolCommand {
val alt = Allele.create(genotypeValues(4))
val start = genotypeValues(2).toInt
val end = ref.length - 1 + start
- val genotypes = samples.toList.zipWithIndex.map { case (sampleName, index) =>
- val gps = Array(
- genotypeValues(5 + (index * 3)),
- genotypeValues(5 + (index * 3) + 1),
- genotypeValues(5 + (index * 3) + 2)
- ).map(_.toDouble)
- val alleles = gps.indexOf(gps.max) match {
- case 0 => List(ref, ref)
- case 1 => List(ref, alt)
- case 2 => List(alt, alt)
- }
- new GenotypeBuilder()
- .name(sampleName)
- .alleles(alleles)
- .attribute("GP", gps)
- .PL(gps)
- .make()
+ val genotypes = samples.toList.zipWithIndex.map {
+ case (sampleName, index) =>
+ val gps = Array(
+ genotypeValues(5 + (index * 3)),
+ genotypeValues(5 + (index * 3) + 1),
+ genotypeValues(5 + (index * 3) + 2)
+ ).map(_.toDouble)
+ val alleles = gps.indexOf(gps.max) match {
+ case 0 => List(ref, ref)
+ case 1 => List(ref, alt)
+ case 2 => List(alt, alt)
+ }
+ new GenotypeBuilder()
+ .name(sampleName)
+ .alleles(alleles)
+ .attribute("GP", gps)
+ .PL(gps)
+ .make()
}
val builder = (new VariantContextBuilder)
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 9e8d529b7d4d9f67fb282163b3bcc5d96dfb8858..df2af5d9ee37cd1daabcd62214ab67577ce3491a 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
@@ -2,16 +2,16 @@ package nl.lumc.sasc.biopet.pipelines.gwastest
import java.io.File
-import nl.lumc.sasc.biopet.core.{PipelineCommand, Reference, BiopetQScript}
-import nl.lumc.sasc.biopet.extensions.gatk.{SelectVariants, CombineVariants}
+import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, BiopetQScript }
+import nl.lumc.sasc.biopet.extensions.gatk.{ SelectVariants, 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
/**
- * Created by pjvanthof on 16/03/16.
- */
+ * Created by pjvanthof on 16/03/16.
+ */
class GwasTest(val root: Configurable) extends QScript with BiopetQScript with Reference {
def this() = this(null)
@@ -24,10 +24,11 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
else {
if (config.contains("input_gens")) {
val gens: List[Any] = configValue2list(config("input_gens"))
- Some(gens.map{ case value: Map[String, Any] =>
- GensInput(new File(value("genotypes").toString),
- value.get("info").map(x => new File(x.toString)),
- value("contig").toString)
+ Some(gens.map {
+ case value: Map[String, Any] =>
+ GensInput(new File(value("genotypes").toString),
+ value.get("info").map(x => new File(x.toString)),
+ value("contig").toString)
})
} else None
}
@@ -60,24 +61,24 @@ class GwasTest(val root: Configurable) extends QScript with BiopetQScript with R
}
val snpTests = BedRecordList.fromReference(referenceFasta())
- .scatter(config("bin_size", default = 10^6))
+ .scatter(config("bin_size", default = 10 ^ 6))
.allRecords.map { region =>
- val regionDir = new File(outputDir, "snptest" + File.separator + region.chr)
- regionDir.mkdirs()
- val bedFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.bed")
- BedRecordList.fromList(List(region)).writeToFile(bedFile)
- bedFile.deleteOnExit()
+ val regionDir = new File(outputDir, "snptest" + File.separator + region.chr)
+ regionDir.mkdirs()
+ val bedFile = new File(regionDir, s"${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(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
- sv.intervals :+= bedFile
- sv.isIntermediate = true
- add(sv)
+ val sv = new SelectVariants(this)
+ sv.inputFiles :+= vcfFile
+ sv.outputFile = new File(regionDir, s"${region.chr}-${region.start + 1}-${region.end}.vcf.gz")
+ sv.intervals :+= bedFile
+ sv.isIntermediate = true
+ add(sv)
- //TODO: snptest
- (region -> "")
- }
+ //TODO: snptest
+ (region -> "")
+ }
}
}