Add basic version of bamstats to pipeline

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

@@ -16,13 +16,13 @@ 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.core.summary.SummaryQScript
-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.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.extensions.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.extensions.tools.{BamStats, 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
@@ -86,6 +86,11 @@ class BamMetrics(val root: Configurable) extends QScript
     add(biopetFlagstat)
     addSummarizable(biopetFlagstat, "biopet_flagstat")
 
+    val bamStats = new BamStats(this)
+    bamStats.bamFile = inputBam
+    bamStats.outputDir = new File(outputDir, "bamstats")
+    add(bamStats)
+
     val multiMetrics = new CollectMultipleMetrics(this)
     multiMetrics.input = inputBam
     multiMetrics.outputName = new File(outputDir, inputBam.getName.stripSuffix(".bam"))

biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BamStats.scala

+package nl.lumc.sasc.biopet.extensions.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.{Reference, ToolCommandFunction}
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.Input
+
+/**
+  * Created by pjvanthof on 18/11/2016.
+  */
+class BamStats(val root: Configurable) extends ToolCommandFunction with Reference {
+  def toolObject = nl.lumc.sasc.biopet.tools.bamstats.BamStats
+
+  @Input(required = true)
+  var reference: File = _
+
+  @Input(required = true)
+  var bamFile: File = _
+
+  var outputDir: File = _
+
+  var binSize: Option[Int] = config("bin_size")
+  var threadBinSize: Option[Int] = config("thread_bin_size")
+
+  override def defaultThreads = 3
+  override def defaultCoreMemory = 5.0
+
+  /** Creates command to execute extension */
+  override def cmdLine = super.cmdLine +
+    required("-b", bamFile) +
+    required("-o", outputDir) +
+    required("-R", reference) +
+    optional("--binSize", binSize),
+    optional("--threadBinSize", threadBinSize)
+
+}