sort input bed and fix test

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.annotations.{ RibosomalRefFlat, AnnotationRefFlat }
+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.{ Reference, BiopetFifoPipe, PipelineCommand, 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.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
@@ -164,7 +164,11 @@ class BamMetrics(val root: Configurable) extends QScript
       addSummarizable(biopetFlagstatLoose, targetName + "_biopet_flagstat_loose")
       add(new BiopetFifoPipe(this, List(biLoose, biopetFlagstatLoose)))
 
-      val bedCov = BedtoolsCoverage(this, intervals.bed, inputBam, depth = true)
+      val sorter = new BedtoolsSort(this)
+      sorter.input = intervals.bed
+      sorter.output = swapExt(targetDir, intervals.bed, ".bed", ".sorted.bed")
+      add(sorter)
+      val bedCov = BedtoolsCoverage(this, sorter.output, inputBam, depth = true)
       val covStats = CoverageStats(this, targetDir, inputBam.getName.stripSuffix(".bam") + ".coverage")
       covStats.title = Some("Coverage Plot")
       covStats.subTitle = Some(s"for file '$targetName.bed'")

biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bedtools/BedtoolsSort.scala

+package nl.lumc.sasc.biopet.extensions.bedtools
+
+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}
+
+
+/**
+  * Created by Sander Bollen on 26-5-16.
+  */
+class BedtoolsSort(val root: Configurable) extends Bedtools with Reference {
+
+  @Input
+  var input: File = null
+
+  @Output
+  var output: File = null
+
+  @Argument(required = false)
+  var faidx: File = referenceFai
+
+
+  def cmdLine = required(executable) + required("sort") + required("-i", input) +
+    optional("-faidx", faidx) +
+    (if(outputAsStsout) "" else " > " + required(output))
+
+}

biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/BedToolsTest.scala

@@ -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
+import nl.lumc.sasc.biopet.utils.config.{Config, Configurable}
 import org.scalatest.Matchers
 import org.scalatest.testng.TestNGSuite
 import org.testng.annotations.Test
@@ -21,10 +21,14 @@ 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()
-    val cov = new BedtoolsCoverage(null) {
-      override def globalConfig = new Config(Map("output_dir" -> tmp.getParent))
+    class TestCov(override val root: Configurable) extends BedtoolsCoverage(root)  {
+      jobTempDir = tmp
+      override def referenceFai = file
+
+      def genome = BedtoolsCoverage.createGenomeFile(file, file.getParentFile)
     }
-    val genome = cov.createGenomeFile(file)
+    val cov = new TestCov(null)
+    val genome = cov.genome
     Source.fromFile(genome).getLines().mkString("\n") shouldBe "chr1\t9"
   }