- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.

- More cleanup including removing the temporary classes and intermediate error files.  Quieting any errors using Apache Commons IO 2.0.
- Counting the contigs during the QScript generation instead of the end user having to pass a separate contig interval list.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4539 348d0f76-0448-11de-a6fe-93d51630548a

ivy.xml

@@ -34,7 +34,7 @@
     <!-- Commons Dependencies -->  
     <dependency org="org.apache.commons" name="commons-jexl" rev="2.0"/>
     <dependency org="commons-logging" name="commons-logging" rev="1.1.1"/>
-    <dependency org="commons-io" name="commons-io" rev="1.3.2"/>
+    <dependency org="commons-io" name="commons-io" rev="2.0"/>
 
     <!-- Dependencies for Queue GATK Extensions code generator living in java/src -->
     <dependency org="commons-lang" name="commons-lang" rev="2.5"/>

scala/qscript/depristo/manySampleUGPerformance.scala

@@ -16,7 +16,7 @@ val MERGED_DIR = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/ma
 trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { 
     this.logging_level = "INFO"; 
     this.jarFile = gatkJarFile;
-    this.intervals :+= new File(TARGET_INTERVAL);
+    this.intervals = List(new File(TARGET_INTERVAL));
     this.reference_sequence = referenceFile; 
     this.jobQueue = "gsa"; 
     this.et = Option(org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD);

scala/qscript/depristo/resequencingSamples1KG.scala

@@ -20,7 +20,7 @@ class ManySampleUGPerformanceTesting extends QScript {
   trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
     this.logging_level = "INFO";
     this.jarFile = gatkJarFile;
-    this.intervals :+= new File(TARGET_INTERVAL);
+    this.intervals = List(new File(TARGET_INTERVAL));
     this.reference_sequence = referenceFile;
     this.jobQueue = "gsa";
     this.et = Option(org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD);

scala/qscript/examples/ExampleUnifiedGenotyper.scala

@@ -41,7 +41,7 @@ class ExampleUnifiedGenotyper extends QScript {
   trait UnifiedGenotyperArguments extends CommandLineGATK {
     this.jarFile = qscript.gatkJar
     this.reference_sequence = qscript.referenceFile
-    this.intervals :+= qscript.intervals
+    this.intervals = List(qscript.intervals)
     // Some() is how you set the value for an scala Option.
     // Set the memory limit to 2 gigabytes on each command.
     this.memoryLimit = Some(2)

scala/qscript/fullCallingPipeline.q

@@ -16,9 +16,6 @@ import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
 class fullCallingPipeline extends QScript {
   qscript =>
 
-  @Argument(doc="list of contigs in the reference over which indel-cleaning jobs should be scattered (ugly)", shortName="contigIntervals")
-  var contigIntervals: File = _
-
   @Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
   var yamlFile: File = _
 
@@ -64,7 +61,7 @@ class fullCallingPipeline extends QScript {
   private var pipeline: Pipeline = _
 
   trait CommandLineGATKArgs extends CommandLineGATK {
-    this.intervals :+= qscript.pipeline.getProject.getIntervalList
+    this.intervals = List(qscript.pipeline.getProject.getIntervalList)
     this.jarFile = qscript.gatkJar
     this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
     this.memoryLimit = Some(4)
@@ -88,10 +85,9 @@ class fullCallingPipeline extends QScript {
     //val expKind = qscript.protocol
 
     // count number of contigs (needed for indel cleaning parallelism)
-    var contigCount = 0
+    val contigCount = IntervalScatterFunction.countContigs(
-    for ( line <- scala.io.Source.fromFile(qscript.contigIntervals).getLines ) {
+      qscript.pipeline.getProject.getReferenceFile,
-      contigCount += 1
+      List(qscript.pipeline.getProject.getIntervalList.toString))
-    }
 
     for ( sample <- recalibratedSamples ) {
       val sampleId = sample.getId
@@ -118,7 +114,6 @@ class fullCallingPipeline extends QScript {
       realigner.jobOutputFile = new File(".queue/logs/Cleaning/%s/IndelRealigner.out".format(sampleId))
       realigner.analysisName = "RealignBam_"+sampleId
       realigner.input_file = targetCreator.input_file
-      realigner.intervals :+= qscript.contigIntervals
       realigner.targetIntervals = targetCreator.out
       realigner.scatterCount = contigCount
 

scala/qscript/recalibrate.scala

@@ -39,7 +39,7 @@ def script = {
           add(new CountCovariates(bamIn, recalData) { useOriginalQualities = true } )
       val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true }
       if ( scatter ) {
-          tableRecal.intervals :+= new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
+          tableRecal.intervals = List(new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list"))
 	  //tableRecal.scatterClass = classOf[ContigScatterFunction]
 	  tableRecal.setupGatherFunction = { case (f: PicardBamJarFunction, _) => f.jarFile = picardMergeSamFilesJar; f.memoryLimit = Some(4) }
       	  tableRecal.scatterCount = 25

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

@@ -75,18 +75,18 @@ class QCommandLine extends CommandLineProgram with Logging {
     }
 
     Runtime.getRuntime.addShutdownHook(new Thread {
-      /** Kills running processes as the JVM shuts down. */
+      /** Cleanup as the JVM shuts down. */
       override def run = {
         qGraph.shutdown()
         ProcessController.shutdown()
+        QScriptManager.deleteOutdir()
       }
     })
 
-    if ( ! getStatus ) {
+    if (getStatus)
-      qGraph.run
-    } else {
       qGraph.checkStatus
-    }
+    else
+      qGraph.run
 
     if (qGraph.hasFailed) {
       logger.info("Done with errors")

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

@@ -11,6 +11,7 @@ import org.apache.log4j.Level
 import scala.tools.nsc.util.{FakePos, NoPosition, Position}
 import org.broadinstitute.sting.utils.classloader.{PackageUtils, PluginManager}
 import org.broadinstitute.sting.queue.util.TextFormatUtils._
+import org.apache.commons.io.FileUtils
 
 /**
  * Plugin manager for QScripts which loads QScripts into the current class loader.
@@ -40,6 +41,8 @@ class QScriptManager extends PluginManager[QScript](classOf[QScript], "QScript",
  * Plugin manager for QScripts which loads QScripts into the current classloader.
  */
 object QScriptManager extends Logging {
+  private val outdir = IOUtils.tempDir("Q-classes")
+
   /**
    * Compiles and loads the scripts in the files into the current classloader.
    * Heavily based on scala/src/compiler/scala/tools/ant/Scalac.scala
@@ -49,7 +52,6 @@ object QScriptManager extends Logging {
     if (scripts.size > 0) {
 
       val settings = new Settings((error: String) => logger.error(error))
-      val outdir = IOUtils.tempDir("Q-classes")
       settings.deprecation.value = true
       settings.outdir.value = outdir.getPath
 
@@ -82,6 +84,14 @@ object QScriptManager extends Logging {
     }
   }
 
+  /**
+   * Removes the outdir cleaning up the temporary classes.
+   */
+  def deleteOutdir() = {
+    if (FileUtils.deleteQuietly(outdir))
+      logger.debug("Deleted " + outdir)
+  }
+
   /**
    * NSC (New Scala Compiler) reporter which logs to Log4J.
    * Heavily based on scala/src/compiler/scala/tools/nsc/reporters/ConsoleReporter.scala

scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.queue.engine
 
 import org.broadinstitute.sting.queue.function.InProcessFunction
-import org.broadinstitute.sting.queue.util.{IOUtils, Logging}
+import org.broadinstitute.sting.queue.util.Logging
 
 /**
  * Runs a function that executes in process and does not fork out an external process.
@@ -17,8 +17,8 @@ class InProcessRunner(val function: InProcessFunction) extends JobRunner with Lo
         logger.info("Starting: " + function.description)
       }
 
-      function.doneOutputs.foreach(_.delete())
+      function.deleteLogs()
-      function.failOutputs.foreach(_.delete())
+      function.deleteOutputs()
       runStatus = RunnerStatus.RUNNING
       function.mkOutputDirectories()
       function.run()

scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.queue.engine
 import java.io.File
 import org.broadinstitute.sting.queue.function.CommandLineFunction
 import org.broadinstitute.sting.queue.util._
+import org.apache.commons.io.FileUtils
 
 /**
  * Runs jobs on an LSF compute cluster.
@@ -72,9 +73,8 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
         logger.info("Starting: " + job.bsubCommand.mkString(" "))
       }
 
-      function.jobOutputFile.delete()
+      function.deleteLogs()
-      if (function.jobErrorFile != null)
+      function.deleteOutputs()
-        function.jobErrorFile.delete()
 
       runStatus = RunnerStatus.RUNNING
       Retry.attempt(() => job.run(), 1, 5, 10)
@@ -139,11 +139,11 @@ class LsfJobRunner(val function: CommandLineFunction) extends DispatchJobRunner
    * Removes all temporary files used for this LSF job.
    */
   def removeTemporaryFiles() = {
-    exec.delete()
+    FileUtils.deleteQuietly(exec)
-    preExec.delete()
+    FileUtils.deleteQuietly(preExec)
-    postExec.delete()
+    FileUtils.deleteQuietly(postExec)
-    jobDoneFile.delete()
+    FileUtils.deleteQuietly(jobDoneFile)
-    jobFailFile.delete()
+    FileUtils.deleteQuietly(jobFailFile)
   }
 
   /**

scala/src/org/broadinstitute/sting/queue/engine/ShellJobRunner.scala

@@ -28,18 +28,11 @@ class ShellJobRunner(val function: CommandLineFunction) extends JobRunner with L
       }
 
       logger.info("Output written to " + function.jobOutputFile)
-      if (function.jobErrorFile != null) {
-        logger.info("Errors written to " + function.jobErrorFile)
-      } else {
-        if (logger.isDebugEnabled)
-          logger.info("Errors also written to " + function.jobOutputFile)
-      }
-
-      function.jobOutputFile.delete()
       if (function.jobErrorFile != null)
-        function.jobErrorFile.delete()
+        logger.info("Errors written to " + function.jobErrorFile)
-      function.doneOutputs.foreach(_.delete())
+
-      function.failOutputs.foreach(_.delete())
+      function.deleteLogs()
+      function.deleteOutputs()
       runStatus = RunnerStatus.RUNNING
       function.mkOutputDirectories()
       job.run()

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

@@ -51,23 +51,43 @@ class IntervalScatterFunction extends ScatterFunction with InProcessFunction {
   }
 
   def run() = {
-    IntervalScatterFunction.scatter(this.intervals, this.scatterParts, this.referenceSequence, this.splitByContig)
+    IntervalScatterFunction.scatter(this.referenceSequence, this.intervals, this.scatterParts, this.splitByContig)
   }
 }
 
 object IntervalScatterFunction {
-  def scatter(intervals: List[String], scatterParts: List[File], reference: File, splitByContig: Boolean) = {
+  private def parseLocs(referenceSource: ReferenceDataSource, intervals: List[String]) = {
-    val referenceSource = new ReferenceDataSource(reference)
     GenomeLocParser.setupRefContigOrdering(referenceSource.getReference)
     val locs = {
       // TODO: Abstract genome analysis engine has richer logic for parsing.  We need to use it!
       if (intervals.size == 0) {
-        GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSource.getReference.getSequenceDictionary).toList
+        GenomeLocSortedSet.createSetFromSequenceDictionary(referenceSource.getReference.getSequenceDictionary)
       } else {
-        IntervalUtils.parseIntervalArguments(intervals, false)
+        new GenomeLocSortedSet(IntervalUtils.parseIntervalArguments(intervals, false))
       }
     }
+    if (locs == null || locs.size == 0)
+      throw new QException("Intervals are empty: " + intervals.mkString(", "))
+    locs.toList
+  }
 
+  def countContigs(reference: File, intervals: List[String]) = {
+    val referenceSource = new ReferenceDataSource(reference)
+    val locs = parseLocs(referenceSource, intervals)
+    var count = 0
+    var contig: String = null
+    for (loc <- locs) {
+      if (contig != loc.getContig) {
+        count += 1
+        contig = loc.getContig
+      }
+    }
+    count
+  }
+
+  def scatter(reference: File, intervals: List[String], scatterParts: List[File], splitByContig: Boolean) = {
+    val referenceSource = new ReferenceDataSource(reference)
+    val locs = parseLocs(referenceSource, intervals)
     val fileHeader = new SAMFileHeader
     fileHeader.setSequenceDictionary(referenceSource.getReference.getSequenceDictionary)
 
@@ -75,9 +95,6 @@ object IntervalScatterFunction {
     var fileIndex = -1
     var locIndex = 0
 
-    if (locs == null || locs.size == 0)
-      throw new QException("Locs produced an empty interval list: " + intervals.mkString(", "))
-
     if (splitByContig) {
       var contig: String = null
       for (loc <- locs) {

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

@@ -3,17 +3,18 @@ package org.broadinstitute.sting.queue.function
 import java.io.File
 import java.lang.annotation.Annotation
 import org.broadinstitute.sting.commandline._
-import org.broadinstitute.sting.queue.util.{CollectionUtils, IOUtils, ReflectionUtils}
 import org.broadinstitute.sting.queue.{QException, QSettings}
 import collection.JavaConversions._
 import org.broadinstitute.sting.queue.function.scattergather.{Gather, SimpleTextGatherFunction}
+import org.broadinstitute.sting.queue.util.{Logging, CollectionUtils, IOUtils, ReflectionUtils}
+import org.apache.commons.io.FileUtils
 
 /**
  * The base interface for all functions in Queue.
  * Inputs and outputs are specified as Sets of values.
  * Inputs are matched to other outputs by using .equals()
  */
-trait QFunction {
+trait QFunction extends Logging {
   /**
    * Analysis function name
    */
@@ -152,13 +153,27 @@ trait QFunction {
     dirs
   }
 
+  /**
+   * Deletes the log files for this function.
+   */
+  def deleteLogs() = {
+    deleteOutput(jobOutputFile)
+    if (jobErrorFile != null)
+      deleteOutput(jobErrorFile)
+  }
+
   /**
    * Deletes the output files and all the status files for this function.
    */
   def deleteOutputs() = {
-    outputs.foreach(_.delete())
+    outputs.foreach(file => deleteOutput(file))
-    doneOutputs.foreach(_.delete())
+    doneOutputs.foreach(file => deleteOutput(file))
-    failOutputs.foreach(_.delete())
+    failOutputs.foreach(file => deleteOutput(file))
+  }
+
+  private def deleteOutput(file: File) = {
+    if (FileUtils.deleteQuietly(file))
+      logger.debug("Deleted " + file)
   }
 
   /**

scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala

@@ -23,7 +23,7 @@ class BamProcessing(yaml: File, gatkJar: File, fixMatesJar: File) {
 
   trait StandardCommandLineGATK extends CommandLineGATK {
     this.reference_sequence = library.attributes.getProject.getReferenceFile
-    this.intervals :+= library.attributes.getProject.getIntervalList
+    this.intervals = List(library.attributes.getProject.getIntervalList)
     this.DBSNP = library.attributes.getProject.getDbsnpFile
     this.memoryLimit = Some(2)
     this.jarFile = library.gatkJar

scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala

@@ -23,7 +23,7 @@ class VariantCalling(yaml: File,gatkJar: File) {
    */
   trait StandardCommandLineGATK extends CommandLineGATK {
     this.reference_sequence = vc.attributes.getProject.getReferenceFile
-    this.intervals :+= vc.attributes.getProject.getIntervalList
+    this.intervals = List(vc.attributes.getProject.getIntervalList)
     this.DBSNP = vc.attributes.getProject.getDbsnpFile
     // set global memory limit on the low side. Additional input bams will affect it.
     this.memoryLimit = Some(2)

scala/test/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunctionUnitTest.scala

@@ -19,6 +19,12 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
     GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary())
   }
 
+  @Test
+  def testCountContigs = {
+    Assert.assertEquals(3, IntervalScatterFunction.countContigs(reference, List("1:1-1", "2:1-1", "3:2-2")))
+    Assert.assertEquals(1, IntervalScatterFunction.countContigs(reference, List(BaseTest.validationDataLocation + "chr1_b36_pilot3.interval_list")))
+  }
+
   @Test
   def testBasicScatter = {
     val chr1 = GenomeLocParser.parseGenomeInterval("1")
@@ -27,7 +33,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "basic." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(List("1", "2", "3"), files, reference, false)
+    IntervalScatterFunction.scatter(reference, List("1", "2", "3"), files, false)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
@@ -51,7 +57,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "less." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(List("1", "2", "3", "4"), files, reference, false)
+    IntervalScatterFunction.scatter(reference, List("1", "2", "3", "4"), files, false)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
@@ -70,7 +76,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
   @Test(expected=classOf[QException])
   def testScatterMoreFiles = {
     val files = (1 to 3).toList.map(index => new File(testDir + "more." + index + ".intervals"))
-    IntervalScatterFunction.scatter(List("1", "2"), files, reference, false)
+    IntervalScatterFunction.scatter(reference, List("1", "2"), files, false)
   }
 
   @Test
@@ -83,7 +89,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "split." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(intervals, files, reference, true)
+    IntervalScatterFunction.scatter(reference, intervals, files, true)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
@@ -99,6 +105,29 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
     Assert.assertEquals(chr3, locs3.get(0))
   }
 
+  @Test
+  def testScatterOrder = {
+    val intervals = List("2:1-1", "1:1-1", "3:2-2")
+    val chr1 = GenomeLocParser.parseGenomeInterval("1:1-1")
+    val chr2 = GenomeLocParser.parseGenomeInterval("2:1-1")
+    val chr3 = GenomeLocParser.parseGenomeInterval("3:2-2")
+
+    val files = (1 to 3).toList.map(index => new File(testDir + "split." + index + ".intervals"))
+
+    IntervalScatterFunction.scatter(reference, intervals, files, true)
+
+    val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
+    val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
+    val locs3 = IntervalUtils.parseIntervalArguments(List(files(2).toString), false)
+
+    Assert.assertEquals(1, locs1.size)
+    Assert.assertEquals(1, locs2.size)
+    Assert.assertEquals(1, locs3.size)
+
+    Assert.assertEquals(chr1, locs1.get(0))
+    Assert.assertEquals(chr2, locs2.get(0))
+    Assert.assertEquals(chr3, locs3.get(0))
+  }
 
   @Test
   def testBasicScatterByContig = {
@@ -108,7 +137,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "contig_basic." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(List("1", "2", "3"), files, reference, true)
+    IntervalScatterFunction.scatter(reference, List("1", "2", "3"), files, true)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
@@ -132,7 +161,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "contig_less." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(List("1", "2", "3", "4"), files, reference, true)
+    IntervalScatterFunction.scatter(reference, List("1", "2", "3", "4"), files, true)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
@@ -151,7 +180,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
   @Test(expected=classOf[QException])
   def testScatterByContigMoreFiles = {
     val files = (1 to 3).toList.map(index => new File(testDir + "contig_more." + index + ".intervals"))
-    IntervalScatterFunction.scatter(List("1", "2"), files, reference, true)
+    IntervalScatterFunction.scatter(reference, List("1", "2"), files, true)
   }
 
   @Test
@@ -164,7 +193,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "contig_split_start." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(intervals, files, reference, true)
+    IntervalScatterFunction.scatter(reference, intervals, files, true)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
@@ -190,7 +219,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "contig_split_middle." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(intervals, files, reference, true)
+    IntervalScatterFunction.scatter(reference, intervals, files, true)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)
@@ -216,7 +245,7 @@ class IntervalScatterFunctionUnitTest extends BaseTest {
 
     val files = (1 to 3).toList.map(index => new File(testDir + "contig_split_end." + index + ".intervals"))
 
-    IntervalScatterFunction.scatter(intervals, files, reference, true)
+    IntervalScatterFunction.scatter(reference, intervals, files, true)
 
     val locs1 = IntervalUtils.parseIntervalArguments(List(files(0).toString), false)
     val locs2 = IntervalUtils.parseIntervalArguments(List(files(1).toString), false)