At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.

No longer generating deprecated GATK arguments on the Queue extensions.
Emitting deprecation warnings to Queue compile to help debugging issues.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java

@@ -110,8 +110,9 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
     public static List<? extends ArgumentField> getArgumentFields(Class<?> classType) {
         List<ArgumentField> argumentFields = new ArrayList<ArgumentField>();
         for (ArgumentSource argumentSource: ParsingEngine.extractArgumentSources(classType))
-            for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions())
+            if (!argumentSource.isDeprecated())
-                argumentFields.addAll(getArgumentFields(argumentDefinition));
+                for (ArgumentDefinition argumentDefinition: argumentSource.createArgumentDefinitions())
+                    argumentFields.addAll(getArgumentFields(argumentDefinition));
         return argumentFields;
     }
 
@@ -131,7 +132,7 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
             //return Collections.<ArgumentField>emptyList();
 
         } else if ("input_file".equals(argumentDefinition.fullName) && argumentDefinition.ioType == ArgumentIOType.INPUT) {
-            return Arrays.asList(new InputNamedFileDefinitionField(argumentDefinition), new IndexFilesField());
+            return Arrays.asList(new InputTaggedFileDefinitionField(argumentDefinition), new IndexFilesField());
 
         } else if (argumentDefinition.ioType == ArgumentIOType.INPUT) {
             return Collections.singletonList(new InputArgumentField(argumentDefinition));
@@ -327,15 +328,15 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
     /**
      * Named input_files.
      */
-    public static class InputNamedFileDefinitionField extends ArgumentDefinitionField {
+    public static class InputTaggedFileDefinitionField extends ArgumentDefinitionField {
-        public InputNamedFileDefinitionField(ArgumentDefinition argumentDefinition) {
+        public InputTaggedFileDefinitionField(ArgumentDefinition argumentDefinition) {
             super(argumentDefinition);
         }
-        @Override protected Class<?> getInnerType() { return null; } // NamedFile does not need to be imported.
+        @Override protected Class<?> getInnerType() { return null; } // TaggedFile does not need to be imported.
-        @Override protected String getFieldType() { return "List[NamedFile]"; }
+        @Override protected String getFieldType() { return "List[File]"; }
         @Override protected String getDefaultValue() { return "Nil"; }
         @Override protected String getCommandLineTemplate() {
-            return " + repeat(\"\", %3$s, format=NamedFile.formatCommandLine(\"%1$s\"))";
+            return " + repeat(\"\", %3$s, format=TaggedFile.formatCommandLine(\"%1$s\"))";
         }
     }
 
@@ -354,8 +355,8 @@ public abstract class ArgumentDefinitionField extends ArgumentField {
         @Override protected String getRawFieldName() { return "index_files"; }
         @Override protected String getFreezeFields() {
             return String.format(
-                    "index_files ++= input_file.filter(bam => bam != null && bam.file.getName.endsWith(\".bam\")).map(bam => new File(bam.file.getPath + \".bai\"))%n" +
+                    "index_files ++= input_file.filter(bam => bam != null && bam.getName.endsWith(\".bam\")).map(bam => new File(bam.getPath + \".bai\"))%n" +
-                    "index_files ++= input_file.filter(sam => sam != null && sam.file.getName.endsWith(\".sam\")).map(sam => new File(sam.file.getPath + \".sai\"))%n");
+                    "index_files ++= input_file.filter(sam => sam != null && sam.getName.endsWith(\".sam\")).map(sam => new File(sam.getPath + \".sai\"))%n");
         }
     }
 

scala/qscript/depristo/manySampleUGPerformance.scala

@@ -44,20 +44,20 @@ class Index(bamIn: File) extends SamtoolsIndexFunction {
 
 class MergeBAMs(bamList: File) extends PrintReads with UNIVERSAL_GATK_ARGS {
     this.memoryLimit = Some(3)
-    this.input_file :+= bamList.toNamedFile
+    this.input_file :+= bamList
     this.o = new File(MERGED_DIR + "/" + bamList.getName + ".bam")
   }
 
-class Call(@Input(doc="foo") bamList: File, n: Integer, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
+class Call(@Input(doc="foo") bamList: File, n: Int, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
     @Output(doc="foo") var outVCF: File = new File("%s.%d.%s.vcf".format(bamList.getName, n, name))
     this.memoryLimit = Some(4)
-    this.input_file :+= bamList.toNamedFile
+    this.input_file :+= bamList
     this.jobQueue = "gsa"
     this.stand_call_conf = Option(10.0)
     this.o = outVCF
   }
 
-class SliceList(n: Integer) extends CommandLineFunction {
+class SliceList(n: Int) extends CommandLineFunction {
     @Output(doc="foo") var list: File = new File("bams.%d.list".format(n))
     this.jobQueue = "gsa"
     def commandLine = "head -n %d %s > %s".format(n, FULL_BAM_LIST, list)

scala/qscript/examples/ExampleCountReads.scala

@@ -55,7 +55,7 @@ class ExampleCountReads extends QScript {
         singleCountReads.jarFile = gatkJar
         singleCountReads.reference_sequence = referenceFile
         // ':+' is the scala List append operator
-        singleCountReads.input_file :+= bamFile.toNamedFile
+        singleCountReads.input_file :+= bamFile
         add(singleCountReads)
       }
     }

scala/qscript/examples/ExampleUnifiedGenotyper.scala

@@ -58,7 +58,7 @@ class ExampleUnifiedGenotyper extends QScript {
     // If you are running this on a compute farm, make sure that the Sting/shell
     // folder is in your path to use mergeText.sh and splitIntervals.sh.
     genotyper.scatterCount = 3
-    genotyper.input_file :+= qscript.bamFile.toNamedFile
+    genotyper.input_file :+= qscript.bamFile
     genotyper.out = swapExt(qscript.bamFile, "bam", "unfiltered.vcf")
 
     evalUnfiltered.rodBind :+= RodBind("vcf", "VCF", genotyper.out)

scala/qscript/fullCallingPipeline.q

@@ -80,7 +80,7 @@ class fullCallingPipeline extends QScript {
     val cleanedBase: String = projectBase + ".cleaned"
     val uncleanedBase: String = projectBase + ".uncleaned"
     // there are commands that use all the bam files
-    var cleanBamFiles = List.empty[NamedFile]
+    var cleanBamFiles = List.empty[File]
 
     for ( bam <- qscript.bamFiles ) {
 
@@ -94,7 +94,7 @@ class fullCallingPipeline extends QScript {
       // create the cleaning commands
 
       val targetCreator = new RealignerTargetCreator with CommandLineGATKArgs
-      targetCreator.input_file :+= bam.toNamedFile
+      targetCreator.input_file :+= bam
       targetCreator.out = indel_targets
 
       val realigner = new IndelRealigner with CommandLineGATKArgs
@@ -112,7 +112,7 @@ class fullCallingPipeline extends QScript {
 
       // put clean bams in clean genotypers
 
-      cleanBamFiles :+= realigner.out.toNamedFile
+      cleanBamFiles :+= realigner.out
 
       add(targetCreator,realigner,samtoolsindex)
     }
@@ -122,7 +122,7 @@ class fullCallingPipeline extends QScript {
     endToEnd(cleanedBase,cleanBamFiles)
   }
 
-  def endToEnd(base: String, bamFiles: List[NamedFile]) = {
+  def endToEnd(base: String, bamFiles: List[File]) = {
 
     // step through the un-indel-cleaned graph:
     // 1a. call snps and indels
@@ -158,7 +158,7 @@ class fullCallingPipeline extends QScript {
     var priority = ""
     for ( bam <- bamFiles ) {
       val indel = new IndelGenotyperV2 with CommandLineGATKArgs
-      indel.input_file :+= bam.toNamedFile
+      indel.input_file :+= bam
       indel.out = swapExt(bam,".bam",".indels.vcf")
       indel.downsample_to_coverage = Some(500)
       indelCallFiles :+= RodBind("v"+loopNo.toString, "VCF", indel.out)
@@ -186,28 +186,28 @@ class fullCallingPipeline extends QScript {
     annotated.rodBind :+= RodBind("variant", "VCF", snps.out)
     annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.refseqTable)
     annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
-    annotated.vcfOutput = swapExt(snps.out,".vcf",".annotated.vcf").getAbsolutePath
+    annotated.out = swapExt(snps.out,".vcf",".annotated.vcf")
     annotated.select :+= "dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet"
     annotated.rodToIntervalTrackName = "variant"
 
 
     // 2.a filter on cluster and near indels
     val masker = new VariantFiltration with CommandLineGATKArgs
-    masker.rodBind :+= RodBind("variant", "VCF", new File(annotated.vcfOutput))
+    masker.rodBind :+= RodBind("variant", "VCF", annotated.out)
-    masker.rodBind :+= RodBind("mask", "VCF", new File(mergeIndels.out.getAbsolutePath))
+    masker.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
     masker.maskName = "NearIndel"
     masker.clusterWindowSize = Some(qscript.snpClusterWindow)
     masker.clusterSize = Some(qscript.snpsInCluster)
-    masker.out = swapExt(new File(annotated.vcfOutput),".vcf",".indel.masked.vcf")
+    masker.out = swapExt(annotated.out,".vcf",".indel.masked.vcf")
 
 
     // 2.b hand filter with standard filter
     val handFilter = new VariantFiltration with CommandLineGATKArgs
-    handFilter.rodBind :+= RodBind("variant", "VCF", new File(annotated.vcfOutput))
+    handFilter.rodBind :+= RodBind("variant", "VCF", annotated.out)
     handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
     handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
     handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","QD<5","\"HRun>=4\"")
-    handFilter.out = swapExt(new File(annotated.vcfOutput),".vcf",".handfiltered.vcf")
+    handFilter.out = swapExt(annotated.out,".vcf",".handfiltered.vcf")
 
 
     // 3.i generate gaussian clusters on the masked vcf

scala/qscript/kshakir/CleanBamFile.scala

@@ -131,16 +131,12 @@ class CleanBamFile extends QScript {
     var fixedBam: File = null
 
     if (realigner.scatterCount > 1) {
-      realigner.output = baseFile(".cleaned.bam")
+      realigner.out = baseFile(".cleaned.bam")
       // While gathering run fix mates.
       realigner.setupScatterFunction = {
         case (scatter: IntervalScatterFunction, _) =>
           scatter.splitIntervalsScript = indelRealignerScatterScript
       }
-      realigner.gatherClass = {
-        case source if (source.field.getName=="output") =>
-          classOf[BamGatherFunction]
-      }
       realigner.setupGatherFunction = {
         case (gather: BamGatherFunction, _) =>
           gather.memoryLimit = Some(4)
@@ -151,9 +147,9 @@ class CleanBamFile extends QScript {
           gather.mergeTextScript = mergeTextScript
       }
 
-      fixedBam = realigner.output
+      fixedBam = realigner.out
     } else {
-      realigner.output = baseFile(".unfixed.cleaned.bam")
+      realigner.out = baseFile(".unfixed.cleaned.bam")
 
       // Explicitly run fix mates if the function won't be scattered.
       var fixMates = new PicardBamJarFunction {
@@ -165,7 +161,7 @@ class CleanBamFile extends QScript {
       }
       fixMates.memoryLimit = Some(4)
       fixMates.jarFile = fixMatesJar
-      fixMates.unfixed = realigner.output
+      fixMates.unfixed = realigner.out
       fixMates.fixed = baseFile(".cleaned.bam")
 
       fixedBam = fixMates.fixed

scala/qscript/recalibrate.scala

@@ -64,7 +64,6 @@ class CountCovariates(bamIn: File, recalDataIn: File) extends org.broadinstitute
     this.recal_file = recalDataIn
     this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod")
     this.logging_level = "INFO"
-    this.max_reads_at_locus = Some(20000)
     this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
     this.memoryLimit = Some(3)
     
@@ -75,7 +74,7 @@ class TableRecalibrate(bamInArg: File, recalDataIn: File, bamOutArg: File) exten
     this.jarFile = gatkJarFile
     this.input_file :+= bamInArg
     this.recal_file = recalDataIn
-    this.output_bam = bamOutArg
+    this.out = bamOutArg
     this.logging_level = "INFO"
     this.memoryLimit = Some(2)
     this.skipUQUpdate = skipUQUpdateArg

scala/qscript/rpoplin/variantRecalibrator.scala

@@ -26,24 +26,23 @@ for (g: Int <- gList) {
         gvc.logging_level = "INFO"
         gvc.intervalsString :+= "20"
         gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
-        gvc.path_to_resources = "/humgen/gsa-scr1/rpoplin/sting_dev_vb/R/"
         gvc.maxGaussians = Some(g)
         gvc.shrinkage = Some(s)
         gvc.shrinkageFormat = "%.6f"
         gvc.dirichlet = Some(d)
         gvc.dirichletFormat = "%.6f"
-        gvc.clusterFile = "g%d_s%.6f_d%.6f_b%.2f.cluster".format(g,s,d,b)
+        gvc.clusterFile = new File("g%d_s%.6f_d%.6f_b%.2f.cluster".format(g,s,d,b))
-        gvc.jobOutputFile = new File(gvc.clusterFile.stripSuffix(".cluster") + ".gvc.out")
+        gvc.jobOutputFile = swapExt(gvc.clusterFile, ".cluster", ".gvc.out")
 
         vr.jarFile = gatkJarFile
         vr.rodBind :+= RodBind("input20", "VCF", new File("/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf"))
         vr.logging_level = "INFO"
         vr.intervalsString :+= "20"
-        vr.target_titv = Some(2.1)
+        vr.target_titv = 2.1
         vr.ignore_filter :+= "HARD_TO_VALIDATE"
         vr.path_to_resources = "/humgen/gsa-scr1/rpoplin/sting_dev_vb/R/"
         vr.clusterFile = gvc.clusterFile
-        vr.jobOutputFile = new File(vr.clusterFile.stripSuffix(".cluster") + ".vr.out")
+        vr.jobOutputFile = swapExt(vr.clusterFile, ".cluster", ".vr.out")
         vr.backOff = Some(b)
         vr.backOffFormat = "%.2f"
 

scala/src/org/broadinstitute/sting/queue/QScriptManager.scala

@@ -49,6 +49,7 @@ object QScriptManager extends Logging {
 
       val settings = new Settings((error: String) => logger.error(error))
       val outdir = IOUtils.tempDir("Q-classes")
+      settings.deprecation.value = true
       settings.outdir.value = outdir.getPath
 
       // Set the classpath to the current class path.

scala/src/org/broadinstitute/sting/queue/extensions/gatk/NamedFile.scala

@@ -1,35 +0,0 @@
-package org.broadinstitute.sting.queue.extensions.gatk
-
-import java.io.File
-import org.broadinstitute.sting.queue.function.FileProvider
-
-/**
- * Used to provide -I input_file arguments to the GATK.
- */
-class NamedFile(var file: File, var name: String = null) extends FileProvider {
-  require(file != null, "NamedFile file cannot be null")
-}
-
-/**
- * Used to provide -I input_file arguments to the GATK.
- */
-object NamedFile {
-  /**
-   * Formats the rod binding on the command line.
-   * Used for optional and repeat.
-   * @param cmdLineParam command line parameter, ex: -I
-   * @param prefix unused
-   * @param value NamedFile to add.
-   * @param suffix unused
-   * @return The command line addition.
-   */
-  def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
-    value match {
-      case namedFile: NamedFile =>
-        if (namedFile.name != null)
-          " %s:%s %s".format(cmdLineParam, namedFile.name, namedFile.file)
-        else
-          " %s %s".format(cmdLineParam, namedFile.file)
-    }
-  }
-}

scala/src/org/broadinstitute/sting/queue/extensions/gatk/NamedFileWrapper.scala

@@ -1,8 +0,0 @@
-package org.broadinstitute.sting.queue.extensions.gatk
-
-import java.io.File
-
-class NamedFileWrapper(private val file: File) {
-  def toNamedFile = new NamedFile(file)
-  def toNamedFile(name: String) = new NamedFile(file, name)
-}

scala/src/org/broadinstitute/sting/queue/extensions/gatk/RodBind.scala

@@ -1,21 +1,27 @@
 package org.broadinstitute.sting.queue.extensions.gatk
 
 import java.io.File
-import org.broadinstitute.sting.queue.function.FileProvider
+import org.broadinstitute.sting.queue.function.FileExtension
+import java.lang.String
 
 /**
  * Used to provide -B rodBind arguments to the GATK.
  */
-case class RodBind(var trackName: String, var trackType: String, var file: File) extends FileProvider {
+class RodBind(var trackName: String, var trackType: String, path: String) extends File(path) with FileExtension {
+  def this(trackName: String, trackType: String, file: File) =
+    this(trackName, trackType, file.getPath)
   require(trackName != null, "RodBind trackName cannot be null")
   require(trackType != null, "RodBind trackType cannot be null")
-  require(file != null, "RodBind file cannot be null")
+  def withPath(newPath: String) = new RodBind(trackName, trackType, newPath)
 }
 
 /**
  * Used to provide -B rodBind arguments to the GATK.
  */
 object RodBind {
+  def apply(trackName: String, trackType: String, path: String) = new RodBind(trackName, trackType, path)
+  def apply(trackName: String, trackType: String, file: File) = new RodBind(trackName, trackType, file)
+
   /**
    * Formats the rod binding on the command line.
    * Used for optional and repeat.
@@ -28,7 +34,7 @@ object RodBind {
   def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
     value match {
       case rodBind: RodBind =>
-        " %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.file)
+        " %s:%s,%s %s".format(cmdLineParam, rodBind.trackName, rodBind.trackType, rodBind.getPath)
     }
   }
 }

scala/src/org/broadinstitute/sting/queue/extensions/gatk/TaggedFile.scala

@@ -0,0 +1,39 @@
+package org.broadinstitute.sting.queue.extensions.gatk
+
+import java.io.File
+import org.broadinstitute.sting.queue.function.FileExtension
+
+/**
+ * Used to provide tagged -I input_file arguments to the GATK.
+ */
+class TaggedFile(path: String, val tag: String) extends File(path) with FileExtension {
+  def this(file: File, tag: String) =
+    this(file.getPath, tag)
+  def withPath(path: String) = new TaggedFile(path, tag)
+}
+
+/**
+ * Used to provide -I input_file arguments to the GATK.
+ */
+object TaggedFile {
+  def apply(path: String, tag: String) = new TaggedFile(path, tag)
+  def apply(file: File, tag: String) = new TaggedFile(file, tag)
+
+  /**
+   * Formats the rod binding on the command line.
+   * Used for optional and repeat.
+   * @param cmdLineParam command line parameter, ex: -I
+   * @param prefix unused
+   * @param value TaggedFile to add.
+   * @param suffix unused
+   * @return The command line addition.
+   */
+  def formatCommandLine(cmdLineParam: String)(prefix: String, value: Any, suffix: String) = {
+    value match {
+      case taggedFile: TaggedFile if (taggedFile.tag != null) =>
+          " %s:%s %s".format(cmdLineParam, taggedFile.tag, taggedFile.getPath)
+      case file: File =>
+          " %s %s".format(cmdLineParam, file.getPath)
+    }
+  }
+}

scala/src/org/broadinstitute/sting/queue/extensions/gatk/package.scala

@@ -1,13 +0,0 @@
-package org.broadinstitute.sting.queue.extensions
-
-import java.io.File
-import org.broadinstitute.sting.queue.extensions.gatk.NamedFile
-import org.broadinstitute.sting.queue.extensions.gatk.NamedFileWrapper
-
-package object gatk {
-  implicit def fileToNamedFileWrapper(file: File) = new NamedFileWrapper(file)
-  // TODO: Get the syntax right so that the implicits kick in for a generic type, ex: Travesable[File], Traversable[_ <: File], etc.
-  // but need to return the same outter type, so T <: Traversable[File] : T[NamedFile], T <: Traversable[_ <: File]: T[NamedFile], etc.
-  implicit def filesToNamedFilesWrapper(files: List[File]) = files.map(file => if (file == null) null else new NamedFile(file))
-  implicit def filesToNamedFilesWrapper(files: Set[File]) = files.map(file => if (file == null) null else new NamedFile(file))
-}

scala/src/org/broadinstitute/sting/queue/function/CommandLineFunction.scala

@@ -94,7 +94,7 @@ trait CommandLineFunction extends QFunction with Logging {
   def outputs = getFieldFiles(outputFields)
 
   /**
-   * Gets the files from the fields.  The fields must be a File, a FileProvider, or a List or Set of either.
+   * Gets the files from the fields.  The fields must be a File, a FileExtension, or a List or Set of either.
    * @param fields Fields to get files.
    * @return Set[File] for the fields.
    */
@@ -121,7 +121,7 @@ trait CommandLineFunction extends QFunction with Logging {
   }
 
   /**
-   * Gets the files from the field.  The field must be a File, a FileProvider, or a List or Set of either.
+   * Gets the files from the field.  The field must be a File, a FileExtension, or a List or Set of either.
    * @param fields Field to get files.
    * @return Set[File] for the field.
    */
@@ -136,7 +136,7 @@ trait CommandLineFunction extends QFunction with Logging {
   }
 
   /**
-   * Gets the file from the field.  The field must be a File or a FileProvider and not a List or Set.
+   * Gets the file from the field.  The field must be a File or a FileExtension and not a List or Set.
    * @param field Field to get the file.
    * @return File for the field.
    */
@@ -144,17 +144,16 @@ trait CommandLineFunction extends QFunction with Logging {
     fieldValueToFile(field, getFieldValue(field))
 
   /**
-   * Converts the field value to a file.  The field must be a File or a FileProvider.
+   * Converts the field value to a file.  The field must be a File or a FileExtension.
    * @param field Field to get the file.
-   * @param value Value of the File or FileProvider or null.
+   * @param value Value of the File or FileExtension or null.
    * @return Null if value is null, otherwise the File.
-   * @throws QException if the value is not a File or FileProvider.
+   * @throws QException if the value is not a File or FileExtension.
    */
   private def fieldValueToFile(field: ArgumentSource, value: Any): File = value match {
     case file: File => file
-    case fileProvider: FileProvider => fileProvider.file
     case null => null
-    case unknown => throw new QException("Non-file found.  Try removing the annotation, change the annotation to @Argument, or implement FileProvider: %s: %s".format(field.field, unknown))
+    case unknown => throw new QException("Non-file found.  Try removing the annotation, change the annotation to @Argument, or extend File with FileExtension: %s: %s".format(field.field, unknown))
   }
 
   /**
@@ -164,15 +163,19 @@ trait CommandLineFunction extends QFunction with Logging {
    */
   def resetFieldFile(field: ArgumentSource, tempDir: File): File = {
     getFieldValue(field) match {
+      case fileExtension: FileExtension => {
+        val newFile = IOUtils.resetParent(tempDir, fileExtension)
+        val newFileExtension = fileExtension.withPath(newFile.getPath)
+        setFieldValue(field, newFileExtension)
+        newFileExtension
+      }
       case file: File => {
+        if (file.getClass == classOf[File])
+          throw new QException("Extensions of file must also extend with FileExtension so that the path can be modified.");
         val newFile = IOUtils.resetParent(tempDir, file)
         setFieldValue(field, newFile)
         newFile
       }
-      case fileProvider: FileProvider => {
-        fileProvider.file = IOUtils.resetParent(tempDir, fileProvider.file)
-        fileProvider.file
-      }
       case null => null
       case unknown =>
         throw new QException("Unable to set file from %s: %s".format(field, unknown))
@@ -242,8 +245,14 @@ trait CommandLineFunction extends QFunction with Logging {
    */
   protected def canon(value: Any) = {
     value match {
-      case file: File => absolute(file)
+      case fileExtension: FileExtension =>
-      case fileProvider: FileProvider => fileProvider.file = absolute(fileProvider.file); fileProvider
+        val newFile = absolute(fileExtension);
+        val newFileExtension = fileExtension.withPath(newFile.getPath)
+        newFileExtension
+      case file: File =>
+        if (file.getClass != classOf[File])
+          throw new QException("Extensions of file must also extend with FileExtension so that the path can be modified.");
+        absolute(file)
       case x => x
     }
   }

scala/src/org/broadinstitute/sting/queue/function/FileExtension.scala

@@ -0,0 +1,15 @@
+package org.broadinstitute.sting.queue.function
+
+import java.io.File
+
+/**
+ * An trait for @Input or @Output CommandLineFunction fields that are extensions of files.
+ */
+trait FileExtension extends File {
+  /**
+   * Returns a clone of the FileExtension with the new path.
+   * @param newPath new path for the clone of this FileExtension
+   * @return a clone of the FileExtension with the new path.
+   */
+  def withPath(newPath: String): File
+}

scala/src/org/broadinstitute/sting/queue/function/FileProvider.scala

@@ -1,11 +0,0 @@
-package org.broadinstitute.sting.queue.function
-
-import java.io.File
-
-/**
- * An trait for @Input or @Output CommandLineFunction fields that are not files, but have a File that can be get/set.
- */
-trait FileProvider {
-  /** Gets/Sets the file. */
-  var file: File
-}