Merge branch 'fix-BIOPET-481' into 'develop'

Fixing BIOPET-481



See merge request !486

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala

@@ -14,7 +14,7 @@
  */
 package nl.lumc.sasc.biopet.utils
 
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
 import java.util
 
 import argonaut.Argonaut._

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/package.scala

@@ -15,6 +15,7 @@
 package nl.lumc.sasc.biopet
 
 import scala.util.{ Failure, Success, Try }
+import scala.math._
 
 /**
  * General utility functions.
@@ -29,6 +30,15 @@ package object utils {
   /** Regular expression for matching entire decimal numbers (compatible with the scientific notation) */
   val isDecimal = """^([-+]?\d*\.?\d+(?:[eE][-+]?[0-9]+)?)$""".r
 
+  def textToSize(text: String): Long = {
+    text.last match {
+      case 'g' | 'G' => ((1L << 30) * text.stripSuffix("g").stripSuffix("G").toDouble).toLong
+      case 'm' | 'M' => ((1L << 20) * text.stripSuffix("g").stripSuffix("G").toDouble).toLong
+      case 'k' | 'K' => ((1L << 10) * text.stripSuffix("g").stripSuffix("G").toDouble).toLong
+      case _         => text.toLong
+    }
+  }
+
   /**
    * Tries to convert the given string with the given conversion functions recursively.
    *

mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

@@ -19,11 +19,11 @@ import java.util.Date
 
 import nl.lumc.sasc.biopet.core._
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.extensions.bowtie.{ Bowtie2, Bowtie }
-import nl.lumc.sasc.biopet.extensions.bwa.{ BwaAln, BwaMem, BwaSampe, BwaSamse }
+import nl.lumc.sasc.biopet.extensions.bowtie.{Bowtie, Bowtie2}
+import nl.lumc.sasc.biopet.extensions.bwa.{BwaAln, BwaMem, BwaSampe, BwaSamse}
 import nl.lumc.sasc.biopet.extensions.gmap.Gsnap
 import nl.lumc.sasc.biopet.extensions.hisat.Hisat2
-import nl.lumc.sasc.biopet.extensions.picard.{ AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam }
+import nl.lumc.sasc.biopet.extensions.picard.{AddOrReplaceReadGroups, MarkDuplicates, MergeSamFiles, ReorderSam, SortSam}
 import nl.lumc.sasc.biopet.extensions.tools.FastqSplitter
 import nl.lumc.sasc.biopet.extensions._
 import nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
@@ -31,6 +31,7 @@ import nl.lumc.sasc.biopet.pipelines.bamtobigwig.Bam2Wig
 import nl.lumc.sasc.biopet.pipelines.flexiprep.Flexiprep
 import nl.lumc.sasc.biopet.pipelines.gears.GearsSingle
 import nl.lumc.sasc.biopet.pipelines.mapping.scripts.TophatRecondition
+import nl.lumc.sasc.biopet.utils.textToSize
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.queue.QScript
 
@@ -163,10 +164,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
       if (numberChunks.isEmpty) {
         if (config.contains("numberchunks")) numberChunks = config("numberchunks", default = None)
         else {
-          val chunkSize: Int = config("chunksize", 1 << 30)
+          val chunkSize: String = config("chunksize", default = "5G")
           val filesize = if (inputR1.getName.endsWith(".gz") || inputR1.getName.endsWith(".gzip")) inputR1.length * 3
           else inputR1.length
-          numberChunks = Option(ceil(filesize.toDouble / chunkSize).toInt)
+          numberChunks = Option(ceil(filesize.toDouble / textToSize(chunkSize)).toInt)
         }
       }
       logger.debug("Chunks: " + numberChunks.getOrElse(1))