Merge branch 'fix-samplenames_qiime' into 'develop'

Fix samplenames qiime

Samples in qiime may not contain `_`, this now get replaces to `-` for qiime only.

Also fixed small bug in vcfstats summary.

See merge request !380

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

@@ -86,7 +86,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFunction with Summariz
     Map("info" -> (for (
       line <- Source.fromFile(generalStats).getLines().toList.tail;
       values = line.split("\t") if values.size >= 2 && !values(0).isEmpty
-    ) yield values(0) -> tryToParseNumber(values(1))
+    ) yield values(0) -> tryToParseNumber(values(1)).getOrElse(None)
     ).toMap)
   }
 
@@ -102,7 +102,7 @@ class VcfStats(val root: Configurable) extends ToolCommandFunction with Summariz
     for (s <- 1 until data(0).size) {
       val sample = data(0)(s)
       val stats = Map("genotype" -> (for (f <- 1 until data.length) yield {
-        data(f)(0) -> tryToParseNumber(data(f)(s))
+        data(f)(0) -> tryToParseNumber(data(f)(s)).getOrElse(None)
       }).toMap)
 
       val sum = new Summarizable {

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

@@ -79,7 +79,7 @@ object VcfWithVcf extends ToolCommand {
     logger.info("Init phase")
 
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val reader = new VCFFileReader(commandArgs.inputFile)
     val secondaryReader = new VCFFileReader(commandArgs.secondaryVcf)

public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsQiimeClosed.scala

@@ -57,7 +57,7 @@ class GearsQiimeClosed(val root: Configurable) extends QScript with SummaryQScri
     val splitLib = new SplitLibrariesFastq(this)
     splitLib.input :+= fastqInput
     splitLib.outputDir = new File(outputDir, "split_libraries_fastq")
-    sampleId.foreach(splitLib.sampleIds :+= _)
+    sampleId.foreach(splitLib.sampleIds :+= _.replaceAll("_", "-"))
     add(splitLib)
 
     val closedReference = new PickClosedReferenceOtus(this)