Created RevertSam queue class

Class for the picard tool RevertSam with all the options for queue scripts.
2011-08-22 14:23:39 -04:00 · 2011-08-22 14:23:39 -04:00 · 8aed151a71
parent caebc88e9a
commit 8aed151a71
1 changed files with 52 additions and 0 deletions
--- a/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/extensions/picard/RevertSam.scala
@ -0,0 +1,52 @@
+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 RevertSam extends org.broadinstitute.sting.queue.function.JavaCommandLineFunction with PicardBamFunction {
+  analysisName = "SortSam"
+  javaMainClass = "net.sf.picard.sam.SortSam"
+
+  @Input(shortName = "input", fullName = "input_bam_files", required = true, doc = "The input SAM or BAM files to revert.")
+  var input: List[File] = _
+
+  @Output(shortName = "output", fullName = "output_bam_file", required = true, doc = "The reverted BAM or SAM output file.")
+  var output: File = _
+
+  @Output(shortName = "out_index", fullName = "output_bam_index_file", required = false, doc = "The output bam index")
+  var outputIndex: File = new File(output + ".bai")
+
+  @Argument(shortName = "roq", fullName = "restore_original_qualities", required = false, doc = "True to restore original qualities from the OQ field to the QUAL field if available.")
+  var restoreOriginalQualities: Boolean = true
+
+  @Argument(shortName = "rdi", fullName = "remove_duplicate_information", required = false, doc = "Remove duplicate read flags from all reads. Note that if this is true and REMOVE_ALIGNMENT_INFORMATION==false, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates.")
+  var removeDuplicateInformation: Boolean = true
+
+  @Argument(shortName = "rai", fullName = "remove_alignment_information", required = false, doc = "Remove all alignment information from the file.")
+  var removeAlignmentInformation: Boolean = true
+
+  @Argument(shortName = "atc", fullName = "attributes_to_clear", required = false, doc = "When removing alignment information, the set of optional tags to remove.")
+  var attributesToClear: List[String] = _
+
+  @Argument(shortName = "sa", fullName = "sample_alias", required = false, doc = "The sample alias to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias.")
+  var sampleAlias: String = null
+
+  @Argument(shortName = "ln", fullName = "library_name", required = false, doc = "The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias.")
+
+  override def inputBams = input
+  override def outputBam = output
+  this.createIndex = Some(true)
+  override def commandLine = super.commandLine +
+       conditionalParameter(!restoreOriginalQualities, " RESTORE_ORIGINAL_QUALITIES=false") +
+       conditionalParameter(!removeDuplicateInformation, " REMOVE_DUPLICATE_INFORMATION=false") +
+       conditionalParameter(!removeAlignmentInformation, " REMOVE_ALIGNMENT_INFORMATION=false") +
+       conditionalParameter(!attributesToClear.isEmpty, repeat(" ATTRIBUTE_TO_CLEAR=", attributesToClear)) +
+       conditionalParameter(sampleAlias != null, " SAMPLE_ALIAS=" + sampleAlias)
+}