Adding sampleBamInsertSize (with some error, too be fixed later)

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.SamReaderFactory
+import htsjdk.samtools.{SamReader, SamReaderFactory}
 
 import scala.collection.JavaConversions._
 
@@ -30,4 +30,33 @@ object BamUtils {
     if (temp.map(_._1).distinct.size != temp.size) throw new IllegalArgumentException("Samples has been found twice")
     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 =>
+
+    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
+  }
+
 }