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