Init version of new tool

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

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+import java.util
+
+import htsjdk.tribble.index.IndexCreator
+import htsjdk.variant.variantcontext.writer.{Options, VariantContextWriterBuilder, AsyncVariantContextWriter}
+import htsjdk.variant.vcf._
+import nl.lumc.sasc.biopet.utils.ToolCommand
+
+import scala.io.Source
+
+/**
+  * Created by pjvanthof on 15/03/16.
+  */
+object ImputeToVcf extends ToolCommand {
+
+  case class Args(inputGenotypes: File = null,
+                  inputInfo: Option[File] = None,
+                  outputVcf: File = null,
+                  sampleFile: File = null,
+                  referenceFasta: Option[File] = None) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('g', "inputGenotypes") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(inputGenotypes = x)
+    } text "Input genotypes"
+    opt[File]('i', "inputInfo") maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(inputInfo = Some(x))
+    } text "Input info fields"
+    opt[File]('o', "outputVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(outputVcf = x)
+    } text "Output vcf file"
+    opt[File]('s', "samplesFile") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(sampleFile = x)
+    } text "Samples file"
+    opt[File]('R', "referenceFasta") maxOccurs 1 valueName "<file>" action { (x, c) =>
+      c.copy(referenceFasta = Some(x))
+    } text "reference fasta file"
+  }
+
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs = argsParser.parse(args, Args()).getOrElse(throw new IllegalArgumentException)
+
+    val samples = new util.HashSet[String]()
+    Source.fromFile(cmdArgs.sampleFile).getLines().toArray.drop(2).map(_.split("\t").head).foreach(samples.add(_))
+
+    val metaLines = new util.HashSet[VCFHeaderLine]()
+    metaLines.add(new VCFFormatHeaderLine("PL", VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.Float, ""))
+
+    //TODO: Add reference dict
+    val header = new VCFHeader(metaLines, samples)
+    val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder()
+      .setOutputFile(cmdArgs.outputVcf)
+      .unsetOption(Options.INDEX_ON_THE_FLY)
+      //.setReferenceDictionary(header.getSequenceDictionary)
+      .build)
+    writer.writeHeader(header)
+
+
+
+    writer.close()
+  }
+}