Some fixes with boolean in the pindelvcf wrapper

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

@@ -7,8 +7,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
 
 /**
-  * Created by wyleung on 20-1-16.
-  */
+ * Created by wyleung on 20-1-16.
+ */
 class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version {
   executable = config("exe", default = "pindel2vcf")
 
@@ -20,15 +20,15 @@ class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with R
   def versionCommand = executable + " -h"
 
   /**
-    * Required parameters
-    */
+   * Required parameters
+   */
   @Input
   var reference: File = referenceFasta
 
   @Output
   var outputVCF: File = _
 
-  var referenceDate: String = config("reference_date")
+  var referenceDate: String = config("reference_date", freeVar = false)
 
   override def beforeGraph: Unit = {
     if (reference == null) reference = referenceFasta()
@@ -54,10 +54,10 @@ class PindelVCF(val root: Configurable) extends BiopetCommandLineFunction with R
   var maxInternalRepeatLength: Option[Int] = config("max_internal_repeatlength")
   var maxPostindelRepeats: Option[Int] = config("max_postindel_repeat")
   var maxPostindelRepeatLength: Option[Int] = config("max_postindel_repeatlength")
-  var onlyBalancedSamples: Boolean = config("only_balanced_samples")
-  var somaticP: Boolean = config("somatic_p")
+  var onlyBalancedSamples: Boolean = config("only_balanced_samples", default = false)
+  var somaticP: Boolean = config("somatic_p", default = false)
   var minimumStrandSupport: Option[Int] = config("minimum_strand_support")
-  var gatkCompatible: Boolean = config("gatk_compatible")
+  var gatkCompatible: Boolean = config("gatk_compatible", default = false)
 
   def cmdLine = required(executable) +
     required("--reference_name", referenceSpecies) +

public/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/BamUtils.scala

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.utils
 
 import java.io.File
 
-import htsjdk.samtools.{SamReader, SamReaderFactory}
+import htsjdk.samtools.{ SAMSequenceRecord, SamReader, SamReaderFactory }
 
 import scala.collection.JavaConversions._
 
@@ -31,32 +31,37 @@ object BamUtils {
     temp.toMap
   }
 
-  /**
-    * Estimate the insertsize for each bam file and return Map[<sampleName>, <insertSize>]
-    *
-    * @param bamFiles input bam files
-    * @return
-    */
-  def sampleBamInsertSize(bamFiles: List[File]): Map[File, Float] = bamFiles.map { file =>
+  def contigInsertSize(inputSam: SamReader, contig: SAMSequenceRecord): Int = {
 
-    val inputSam: SamReader = SamReaderFactory.makeDefault.open(file)
+    val insertsizes: Iterator[Int] = for {
+      read <- inputSam.query(contig.getSequenceName, 1, contig.getSequenceLength, true) //.toStream.slice(0, 100).toList
+      insertsize = read.getInferredInsertSize
+      paired = read.getReadPairedFlag
+      bothMapped = (read.getReadUnmappedFlag == false) && (read.getMateUnmappedFlag == false)
+      if paired && bothMapped
+    } yield {
+      insertsize
+    }
+    val contigInsertSize = insertsizes.foldLeft((0.0, 0))((t, r) => (t._1 + r, t._2 + 1))
+    (contigInsertSize._1 / contigInsertSize._2).toInt
+  }
 
+  /**
+   * Estimate the insertsize for each bam file and return Map[<sampleName>, <insertSize>]
+   *
+   * @param bamFiles input bam files
+   * @return
+   */
+  def sampleBamInsertSize(bamFiles: List[File]): Map[File, Int] = bamFiles.map { file =>
+    val inputSam: SamReader = SamReaderFactory.makeDefault.open(file)
     val baminsertsizes = inputSam.getFileHeader.getSequenceDictionary.getSequences.map {
       contig =>
-        val insertsizes: Iterator[Int] = for {
-          read <- inputSam.query( contig.getSequenceName, 1, contig.getSequenceLength, true) //.toStream.slice(0, 100).toList
-          insertsize = read.getInferredInsertSize
-          paired = read.getReadPairedFlag
-          bothMapped = (read.getReadUnmappedFlag == false) && (read.getMateUnmappedFlag == false)
-          if paired && bothMapped
-        } yield {
-          insertsize
-        }
-        val contigInsertSize = insertsizes.foldLeft((0.0,0))((t, r) => (t._1 + r, t._2 +1))
-        contigInsertSize._1 / contigInsertSize._2
-    }.foldLeft((0.0,0))((t, r) => (t._1 + r, t._2 +1))
-
-    file -> baminsertsizes._1 / baminsertsizes._2
-  }
+        val insertSize = BamUtils.contigInsertSize(inputSam, contig)
+
+        Logging.logger.debug(s"Insertsize ${contig}: ${insertSize}")
+        insertSize
+    }
+    file -> (baminsertsizes.sum / baminsertsizes.size)
+  }.toMap
 
 }