Adding SortVcf extension

public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala

+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+package nl.lumc.sasc.biopet.extensions.picard
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
+
+/** Extension for picard SortVcf */
+class SortVcf(val root: Configurable) extends Picard {
+  javaMainClass = new picard.vcf.SortVcf().getClass.getName
+
+  @Input(doc = "Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)", required = true)
+  var input: File = _
+
+  @Output(doc = "Output VCF to be written.", required = true)
+  var output: File = _
+
+  @Argument(doc = "Sequence dictionary to use", required = false)
+  var sequenceDictionary: String = config("sort_order", default = "coordinate")
+
+  /** Returns command to execute */
+  override def cmdLine = super.cmdLine +
+    (if (inputAsStdin) required("INPUT=", new File("/dev/stdin"), spaceSeparated = false)
+    else required("INPUT=", input, spaceSeparated = false)) +
+    (if (outputAsStsout) required("OUTPUT=", new File("/dev/stdout"), spaceSeparated = false)
+    else required("OUTPUT=", output, spaceSeparated = false)) +
+    required("SEQUENCE_DICTIONARY=", sequenceDictionary, spaceSeparated = false)
+}
+
+object SortVcf {
+  /** Returns default SortSam */
+  def apply(root: Configurable, input: File, output: File): SortVcf = {
+    val sortVcf = new SortVcf(root)
+    sortVcf.input = input
+    sortVcf.output = output
+    sortVcf
+  }
+}
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