Update Tabix wrapper

(cherry picked from commit 6ca9d8be)

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Tabix.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
 
 import java.io.File
 
 import nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
 import nl.lumc.sasc.biopet.core.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
- * Created by pjvan_thof on 3/4/15.
+ * Wrapper for the tabix command
+ *
+ * Note that tabix can either index a file (no stdout stream) or retrieve regions from an indexed file (stdout stream)
+ *
  */
 class Tabix(val root: Configurable) extends BiopetCommandLineFunction {
 
-  @Input(doc = "Input files", required = true)
+  @Input(doc = "Input bgzipped file", required = true)
   var input: File = null
 
-  @Output(doc = "Compressed output file", required = true)
-  protected var output: File = null
+  @Output(doc = "Output (for region query)", required = false)
+  var outputQuery: File = null
+
+  @Output(doc = "Output (for indexing)", required = false) // NOTE: it's a def since we can't change the index name ~ it's always input_name + .tbi
+  lazy val outputIndex: File = {
+    require(input != null, "Input must be defined")
+    new File(input.toString + ".tbi")
+  }
+
+  @Argument(doc = "Regions to query", required = false)
+  var regions: List[String] = config("regions", default = List.empty[String])
 
   var p: Option[String] = config("p")
+  var s: Option[Int] = config("s")
+  var b: Option[Int] = config("b")
+  var e: Option[Int] = config("e")
+  var S: Option[Int] = config("S")
+  var c: Option[String] = config("c")
+  var r: Option[File] = config("r")
+  var B: Boolean = config("B", default = false)
+  var zero: Boolean = config("0", default = false)
+  var h: Boolean = config("h", default = false)
+  var l: Boolean = config("l", default = false)
+  var f: Boolean = config("f", default = false)
 
   executable = config("exe", default = "tabix")
-  override val versionExitcode = List(0, 1)
-  override val versionRegex = """Version: (.*)""".r
+
   override def versionCommand = executable
+  override val versionRegex = """Version: (.*)""".r
+  override val versionExitcode = List(0, 1)
+
+  /** Formats that tabix can handle */
+  private val validFormats: Set[String] = Set("gff", "bed", "sam", "vcf", "psltbl")
 
   override def beforeGraph: Unit = {
-    output = new File(input.getAbsolutePath + ".tbi")
+    p match {
+      case Some(fmt) =>
+        require(validFormats.contains(fmt), "-p flag must be one of " + validFormats.mkString(", "))
+      case None => ;
+    }
   }
 
-  def cmdLine = required(executable) +
-    optional("-p", p) +
-    required(input)
-}
\ No newline at end of file
+  def cmdLine = {
+    val baseCommand = required(executable) +
+      optional("-p", p) +
+      optional("-s", s) +
+      optional("-b", b) +
+      optional("-e", e) +
+      optional("-S", S) +
+      optional("-c", c) +
+      optional("-r", r) +
+      conditional(B, "-B") +
+      conditional(zero, "-0") +
+      conditional(h, "-h") +
+      conditional(l, "-l") +
+      conditional(f, "-f") +
+      required(input)
+
+    // query mode ~ we want to output to a file
+    if (regions.nonEmpty) baseCommand + required("", repeat(regions), escape = false) + " > " + required(outputQuery)
+    // indexing mode
+    else baseCommand
+  }
+}