Adding Pindel to ShivaSVCalling

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/Pindel.scala → public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelCaller.scala

@@ -28,7 +28,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
  * Based on version 0.2.5b8
  */
 
-class Pindel(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
+class PindelCaller(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
   executable = config("exe", default = "pindel", freeVar = false)
 
   override def defaultCoreMemory = 3.0
@@ -169,9 +169,9 @@ class Pindel(val root: Configurable) extends BiopetCommandLineFunction with Refe
     optional("--DD_REPORT_DUPLICATION_READS", DD_REPORT_DUPLICATION_READS) +
 }
 
-object Pindel {
-  def apply(root: Configurable, configFile: File, outputDir: File): Pindel = {
-    val caller = new Pindel(root)
+object PindelCaller {
+  def apply(root: Configurable, configFile: File, outputDir: File): PindelCaller = {
+    val caller = new PindelCaller(root)
     caller.config_file = Some(configFile)
     caller.output_prefix = outputDir
     caller

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala

@@ -15,8 +15,9 @@
  */
 package nl.lumc.sasc.biopet.extensions.pindel
 
-import java.io.File
+import java.io.{PrintWriter, File}
 
+import htsjdk.samtools.SamReaderFactory
 import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
 import nl.lumc.sasc.biopet.utils.ToolCommand
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -31,35 +32,20 @@ class PindelConfig(val root: Configurable) extends BiopetJavaCommandLineFunction
   var output: File = _
 
   @Argument(doc = "Insertsize")
-  var insertsize: Option[Int] = _
+  var insertsize: Int = _
+
+  var sampleName: String = _
 
   override def cmdLine = super.cmdLine +
     "-i" + required(input) +
+    "-l" + required(sampleName) +
     "-s" + required(insertsize) +
     "-o" + required(output)
 }
 
 object PindelConfig extends ToolCommand {
-  def apply(root: Configurable, input: File, output: File): PindelConfig = {
-    val conf = new PindelConfig(root)
-    conf.input = input
-    conf.output = output
-    conf
-  }
-
-  def apply(root: Configurable, input: File, outputDir: String): PindelConfig = {
-    val dir = if (outputDir.endsWith("/")) outputDir else outputDir + "/"
-    val outputFile = new File(dir + swapExtension(input.getName))
-    apply(root, input, outputFile)
-  }
-
-  def apply(root: Configurable, input: File): PindelConfig = {
-    apply(root, input, new File(swapExtension(input.getAbsolutePath)))
-  }
-
-  private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".pindel.cfg"
-
-  case class Args(inputbam: File = null, samplelabel: Option[String] = None, insertsize: Option[Int] = None) extends AbstractArgs
+  case class Args(inputbam: File = null, samplelabel: Option[String] = None,
+                  insertsize: Option[Int] = None, output: Option[File] = None) extends AbstractArgs
 
   class OptParser extends AbstractOptParser {
     opt[File]('i', "inputbam") required () valueName "<bamfile/path>" action { (x, c) =>
@@ -71,6 +57,9 @@ object PindelConfig extends ToolCommand {
     opt[Int]('s', "insertsize") valueName "<insertsize>" action { (x, c) =>
       c.copy(insertsize = Some(x))
     } text "Insertsize is missing"
+    opt[Int]('o', "output") valueName "<output>" action { (x, c) =>
+      c.copy(insertsize = Some(x))
+    } text "Output path is missing"
   }
 
   /**
@@ -81,10 +70,26 @@ object PindelConfig extends ToolCommand {
     val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
 
     val input: File = commandArgs.inputbam
+    val output: File = commandArgs.output.getOrElse( new File(input.getAbsoluteFile + ".pindel.cfg") )
+    val insertsize: Int = commandArgs.insertsize.getOrElse(0)
+
+
+    val bamReader = SamReaderFactory.makeDefault().open(input)
+    val writer = new PrintWriter(output)
+    var sampleName: String = ""
+    for( readgroup <- bamReader.getFileHeader.getReadGroups() ) {
+      val rg = bamReader.getFileHeader.getReadGroup( readgroup )
+      writer.write( s"${input.getAbsoluteFile}\t${insertsize}\t${rg.getSample}")
+    }
+    bamReader.close()
+    writer.close()
 
     // the logic here is to pull the libraries stored in the bam file and output this to a pindel config file.
     // see: http://gmt.genome.wustl.edu/packages/pindel/quick-start.html
     // this is called bam-configuration file
+
+    // sampleLabel can be given from the commandline or read from the bam header
+
     /**
      * filename<tab>avg insert size<tab>sample_label or name for reporting
      * tumor_sample_1222.bam<tab>250<tab>TUMOR_1222

public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva
 
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
 import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, SampleLibraryTag }
-import nl.lumc.sasc.biopet.pipelines.shiva.svcallers.{ Delly, Breakdancer, Clever, SvCaller }
+import nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
 import nl.lumc.sasc.biopet.utils.{ BamUtils, Logging }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
@@ -43,7 +43,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
   }
 
   /** Variantcallers requested by the config */
-  protected val configCallers: Set[String] = config("sv_callers", default = Set("breakdancer", "clever", "delly"))
+  protected val configCallers: Set[String] = config("sv_callers", default = Set("breakdancer", "clever", "delly", "pindel"))
 
   /** This will add jobs for this pipeline */
   def biopetScript(): Unit = {
@@ -66,7 +66,7 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
   }
 
   /** Will generate all available variantcallers */
-  protected def callersList: List[SvCaller] = List(new Breakdancer(this), new Clever(this), new Delly(this))
+  protected def callersList: List[SvCaller] = List(new Breakdancer(this), new Clever(this), new Delly(this), new Pindel(this))
 
   /** Location of summary file */
   def summaryFile = new File(outputDir, "ShivaSvCalling.summary.json")

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelPipeline.scala → public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Pindel.scala

@@ -13,71 +13,68 @@
  * license; For commercial users or users who do not want to follow the AGPL
  * license, please contact us to obtain a separate license.
  */
-package nl.lumc.sasc.biopet.extensions.pindel
+package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ BiopetQScript, PipelineCommand }
+import nl.lumc.sasc.biopet.core.{BiopetQScript, PipelineCommand}
+import nl.lumc.sasc.biopet.extensions.pindel.{PindelCaller, PindelCaller$, PindelConfig}
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
 /// Pindel is actually a mini pipeline executing binaries from the pindel package
-class PindelPipeline(val root: Configurable) extends QScript with BiopetQScript {
-  def this() = this(null)
-
-  @Input(doc = "Input file (bam)")
-  var input: File = _
-
-  @Input(doc = "Reference Fasta file")
-  var reference: File = _
+class Pindel(val root: Configurable) extends SvCaller {
+  val name = "pindel"
 
-  @Argument(doc = "Work directory")
-  var workdir: String = _
-
-  //  @Output(doc = "Pindel VCF output")
-  //  lazy val outputvcf: File = {
-  //    new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
-  //  }
-
-  @Output(doc = "Pindel config")
-  lazy val configfile: File = {
-    new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.cfg")
-  }
-  @Output(doc = "Pindel raw output")
-  lazy val outputvcf: File = {
-    new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
-  }
-
-  override def init() {
-  }
+  def this() = this(null)
+//
+//  @Input(doc = "Input file (bam)")
+//  var input: File = _
+//
+//  @Input(doc = "Reference Fasta file")
+//  var reference: File = _
+//
+//  @Argument(doc = "Work directory")
+//  var workdir: String = _
+//
+//  //  @Output(doc = "Pindel VCF output")
+//  //  lazy val outputvcf: File = {
+//  //    new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
+//  //  }
+//
+//  @Output(doc = "Pindel config")
+//  def configfile: File = {
+//    new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.cfg")
+//  }
+//  @Output(doc = "Pindel raw output")
+//  def outputvcf: File = {
+//    new File(workdir + "/" + input.getName.substring(0, input.getName.lastIndexOf(".bam")) + ".pindel.vcf")
+//  }
 
   def biopetScript() {
-    // read config and set all parameters for the pipeline
-    logger.info("Starting Pindel configuration")
+    for ((sample, bamFile) <- inputBams) {
+      val pindelDir = new File(outputDir, sample)
 
-    val cfg = PindelConfig(this, input, this.configfile)
-    outputFiles += ("pindel_cfg" -> cfg.output)
-    add(cfg)
+      val config_file: File = new File( bamFile.getAbsolutePath + ".pindel.cfg" )
+      val cfg = new PindelConfig(this)
+      cfg.input = bamFile
 
-    val output: File = this.outputvcf
-    val pindel = Pindel(this, cfg.output, output)
-    add(pindel)
-    outputFiles += ("pindel_tsv" -> pindel.output)
+      // FIXME: get the real insert size of the bam (from bammetrics?)
+      cfg.insertsize = 500
+      cfg.sampleName = sample
+      cfg.output = config_file
+      add(cfg)
 
-    //    val output_vcf: File = this.outputvcf
-    // convert this tsv to vcf using the python script
+      val pindel = PindelCaller(this, cfg.output, pindelDir)
+      add(pindel)
+    }
 
   }
-
-  //  private def swapExtension(inputFile: String) = inputFile.substring(0, inputFile.lastIndexOf(".bam")) + ".pindel.tsv"
 }
 
-object PindelPipeline extends PipelineCommand {
-  def apply(root: Configurable, input: File, reference: File, runDir: String): PindelPipeline = {
-    val pindel = new PindelPipeline(root)
-    pindel.input = input
-    pindel.reference = reference
-    pindel.workdir = runDir
+object Pindel extends PipelineCommand {
+  def apply(root: Configurable, input: File, reference: File, runDir: String): Pindel = {
+    val pindel = new Pindel(root)
     // run the following for activating the pipeline steps
     pindel.init()
     pindel.biopetScript()