Added auto `sortInput` on retry

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

@@ -45,6 +45,8 @@ class GensToVcf(val root: Configurable) extends ToolCommandFunction with Referen
 
   var contig: String = _
 
+  var sortInput: Boolean = false
+
   override def defaultCoreMemory = 5.0
 
   override def beforeGraph(): Unit = {
@@ -54,13 +56,19 @@ class GensToVcf(val root: Configurable) extends ToolCommandFunction with Referen
     if (outputVcf.getName.endsWith(".vcf.gz")) outputFiles :+= new File(outputVcf.getAbsolutePath + ".tbi")
   }
 
+  override def setupRetry(): Unit = {
+    super.setupRetry()
+    sortInput = true
+  }
+
   override def cmdLine = super.cmdLine +
     required("--inputGenotypes", inputGens) +
     required("--inputInfo", inputInfo) +
     required("--outputVcf", outputVcf) +
     optional("--contig", contig) +
     required("--referenceFasta", reference) +
-    required("--samplesFile", samplesFile)
+    required("--samplesFile", samplesFile) +
+    conditional(sortInput, "--sortInput")
 
 }
 

public/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GensToVcf.scala

@@ -5,7 +5,7 @@ import java.util
 
 import htsjdk.samtools.reference.{ FastaSequenceFile, ReferenceSequenceFileFactory }
 import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
-import htsjdk.variant.variantcontext.{VariantContext, Allele, GenotypeBuilder, VariantContextBuilder}
+import htsjdk.variant.variantcontext.{ VariantContext, Allele, GenotypeBuilder, VariantContextBuilder }
 import htsjdk.variant.vcf._
 import nl.lumc.sasc.biopet.utils.ToolCommand
 
@@ -44,7 +44,7 @@ object GensToVcf extends ToolCommand {
     opt[String]('c', "contig") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
       c.copy(contig = x)
     } text "contig of impute file"
-    opt[Unit]("sort") maxOccurs 1 action { (x, c) =>
+    opt[Unit]("sortInput") maxOccurs 1 action { (x, c) =>
       c.copy(sortInput = true)
     } text "In memory sorting"
   }
@@ -86,13 +86,13 @@ object GensToVcf extends ToolCommand {
     val lineIt: Iterator[Line] = {
       val it = infoIt match {
         case Some(x) => genotypeIt.zip(x).map(x => Line(x._1, Some(x._2)))
-        case _ => genotypeIt.map(x => Line(x, None))
+        case _       => genotypeIt.map(x => Line(x, None))
       }
 
       if (cmdArgs.sortInput) {
         logger.info("Start Sorting input files")
         val list = it.toList
-        val pos = list.map{ line =>
+        val pos = list.map { line =>
           val values = line.genotype.split(" ")
           val p = values(2).toInt
           val alt = values(4)
@@ -100,8 +100,7 @@ object GensToVcf extends ToolCommand {
           else p
         }
         list.zip(pos).sortBy(_._2).map(_._1).toIterator
-      }
-      else it
+      } else it
     }
 
     logger.info("Start processing genotypes")