Commit 92a3a1b7 authored by Sander Bollen's avatar Sander Bollen
Browse files

autostyle fixes

parent 33c611e0
......@@ -18,17 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.File
import nl.lumc.sasc.biopet.core.annotations.{ AnnotationRefFlat, RibosomalRefFlat }
import nl.lumc.sasc.biopet.core.annotations.{AnnotationRefFlat, RibosomalRefFlat}
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.summary.SummaryQScript
import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag }
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
import nl.lumc.sasc.biopet.core.{BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag}
import nl.lumc.sasc.biopet.extensions.bedtools.{BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort}
import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect, BedtoolsSort }
import nl.lumc.sasc.biopet.extensions.picard._
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedCheck
import org.broadinstitute.gatk.queue.QScript
......
......@@ -84,9 +84,9 @@ object BedtoolsCoverage {
}
/**
* Creates the genome file. i.e. the first two columns of the fasta index
* @return
*/
* Creates the genome file. i.e. the first two columns of the fasta index
* @return
*/
def createGenomeFile(fai: File, dir: File): File = {
val tmp = File.createTempFile(fai.getName, ".genome", dir)
tmp.deleteOnExit()
......
......@@ -4,12 +4,11 @@ import java.io.File
import nl.lumc.sasc.biopet.core.Reference
import nl.lumc.sasc.biopet.utils.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
/**
* Created by Sander Bollen on 26-5-16.
*/
* Created by Sander Bollen on 26-5-16.
*/
class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {
@Input
......@@ -21,9 +20,8 @@ class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {
@Argument(required = false)
var faidx: File = referenceFai
def cmdLine = required(executable) + required("sort") + required("-i", input) +
optional("-faidx", faidx) +
(if(outputAsStsout) "" else " > " + required(output))
(if (outputAsStsout) "" else " > " + required(output))
}
......@@ -118,7 +118,7 @@ object CleverFixVCF extends ToolCommand {
*/
def main(args: Array[String]): Unit = {
val argsParser = new OptParser
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val input: File = commandArgs.inputVCF
val output: File = commandArgs.outputVCF
......
......@@ -4,7 +4,7 @@ import java.io.File
import java.nio.file.Paths
import nl.lumc.sasc.biopet.extensions.bedtools.BedtoolsCoverage
import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
import nl.lumc.sasc.biopet.utils.config.{ Config, Configurable }
import org.scalatest.Matchers
import org.scalatest.testng.TestNGSuite
import org.testng.annotations.Test
......@@ -21,7 +21,7 @@ class BedToolsTest extends TestNGSuite with Matchers {
val file = new File(Paths.get(this.getClass.getResource("/ref.fa.fai").toURI).toString)
val tmp = File.createTempFile("test", ".bed")
tmp.deleteOnExit()
class TestCov(override val root: Configurable) extends BedtoolsCoverage(root) {
class TestCov(override val root: Configurable) extends BedtoolsCoverage(root) {
jobTempDir = tmp
override def referenceFai = file
......
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