Added ReorderSam queue binding

public/scala/src/org/broadinstitute/sting/queue/extensions/picard/ReorderSam.scala

@@ -0,0 +1,48 @@
+package org.broadinstitute.sting.queue.extensions.picard
+
+import org.broadinstitute.sting.commandline._
+
+import java.io.File
+/*
+ * Created by IntelliJ IDEA.
+ * User: carneiro
+ * Date: 6/22/11
+ * Time: 10:35 AM
+ */
+class ReorderSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction {
+  analysisName = "ReorderSam"
+  javaMainClass = "net.sf.picard.sam.SortSam"
+
+  @Input(doc="Input file (bam or sam) to extract reads from.", shortName = "input", fullName = "input_bam_files", required = true)
+  var input: List[File] = Nil
+
+  @Output(doc="Output file (bam or sam) to write extracted reads to.", shortName = "output", fullName = "output_bam_file", required = true)
+  var output: File = _
+
+  @Output(doc="The output bam index", shortName = "out_index", fullName = "output_bam_index_file", required = false)
+  var outputIndex: File = _
+
+  @Argument(doc="Reference sequence to reorder reads to match.", shortName = "input", fullName = "input_bam_files", required = true)
+  var reference: File = _
+
+  @Argument(doc="If true, then allows only a partial overlap of the BAM contigs with the new reference sequence contigs. By default, this tool requires a corresponding contig in the new reference for each read contig.", shortName = "aic", fullName = "allow_incomplete_concordance", required = false)
+  var ALLOW_INCOMPLETE_DICT_CONCORDANCE: Boolean = false
+
+  @Argument(doc="If true, then permits mapping from a read contig to a new reference contig with the same name but a different length. Highly dangerous, only use if you know what you are doing.", shortName = "acld", fullName = "allow_contig_length_discordance", required = false)
+  var ALLOW_CONTIG_LENGTH_DISCORDANCE: Boolean = false
+
+  override def freezeFieldValues() {
+    super.freezeFieldValues()
+    if (outputIndex == null && output != null && output.toString.endsWith(".bam"))
+      outputIndex = new File(output.getName.stripSuffix(".bam") + ".bai")
+  }
+
+  override def inputBams = input
+  override def outputBam = output
+  this.createIndex = Some(outputIndex != null)
+  this.sortOrder = null
+  override def commandLine = super.commandLine +
+    " REFERENCE=" + reference +
+    conditionalParameter (ALLOW_INCOMPLETE_DICT_CONCORDANCE, " ALLOW_INCOMPLETE_DICT_CONCORDANCE=true")
+    conditionalParameter (ALLOW_CONTIG_LENGTH_DISCORDANCE, " ALLOW_CONTIG_LENGTH_DISCORDANCE=true")
+}