diff --git a/ivy.xml b/ivy.xml index e46e02cb2..f4a8f1d8c 100644 --- a/ivy.xml +++ b/ivy.xml @@ -34,7 +34,7 @@ - + diff --git a/scala/qscript/depristo/manySampleUGPerformance.scala b/scala/qscript/depristo/manySampleUGPerformance.scala index 117763a79..e589afd10 100755 --- a/scala/qscript/depristo/manySampleUGPerformance.scala +++ b/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); diff --git a/scala/qscript/depristo/resequencingSamples1KG.scala b/scala/qscript/depristo/resequencingSamples1KG.scala index 24def504f..4837e8af1 100644 --- a/scala/qscript/depristo/resequencingSamples1KG.scala +++ b/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); diff --git a/scala/qscript/examples/ExampleUnifiedGenotyper.scala b/scala/qscript/examples/ExampleUnifiedGenotyper.scala index 3397d03a4..0e4dc6149 100644 --- a/scala/qscript/examples/ExampleUnifiedGenotyper.scala +++ b/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) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index bc73c23eb..a5099e26c 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/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 - for ( line <- scala.io.Source.fromFile(qscript.contigIntervals).getLines ) { - contigCount += 1 - } + val contigCount = IntervalScatterFunction.countContigs( + qscript.pipeline.getProject.getReferenceFile, + 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 diff --git a/scala/qscript/recalibrate.scala b/scala/qscript/recalibrate.scala index 6d9464f4a..5026a3bee 100755 --- a/scala/qscript/recalibrate.scala +++ b/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 diff --git a/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala b/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala index c86a40f52..ee9a35448 100755 --- a/scala/src/org/broadinstitute/sting/queue/QCommandLine.scala +++ b/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 ) { - qGraph.run - } else { + if (getStatus) qGraph.checkStatus - } + else + qGraph.run if (qGraph.hasFailed) { logger.info("Done with errors") diff --git a/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala b/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala index eb8ea710a..9dfbb481c 100644 --- a/scala/src/org/broadinstitute/sting/queue/QScriptManager.scala +++ b/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 diff --git a/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala index 73f4be6dd..5072ffc88 100644 --- a/scala/src/org/broadinstitute/sting/queue/engine/InProcessRunner.scala +++ b/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.failOutputs.foreach(_.delete()) + function.deleteLogs() + function.deleteOutputs() runStatus = RunnerStatus.RUNNING function.mkOutputDirectories() function.run() diff --git a/scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala index 30b73c412..59f9f9baa 100644 --- a/scala/src/org/broadinstitute/sting/queue/engine/LsfJobRunner.scala +++ b/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() - if (function.jobErrorFile != null) - function.jobErrorFile.delete() + function.deleteLogs() + function.deleteOutputs() 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() - preExec.delete() - postExec.delete() - jobDoneFile.delete() - jobFailFile.delete() + FileUtils.deleteQuietly(exec) + FileUtils.deleteQuietly(preExec) + FileUtils.deleteQuietly(postExec) + FileUtils.deleteQuietly(jobDoneFile) + FileUtils.deleteQuietly(jobFailFile) } /** diff --git a/scala/src/org/broadinstitute/sting/queue/engine/ShellJobRunner.scala b/scala/src/org/broadinstitute/sting/queue/engine/ShellJobRunner.scala index b5efdbe7d..aecb79619 100755 --- a/scala/src/org/broadinstitute/sting/queue/engine/ShellJobRunner.scala +++ b/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() - function.doneOutputs.foreach(_.delete()) - function.failOutputs.foreach(_.delete()) + logger.info("Errors written to " + function.jobErrorFile) + + function.deleteLogs() + function.deleteOutputs() runStatus = RunnerStatus.RUNNING function.mkOutputDirectories() job.run() diff --git a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala b/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala index 2fb327e3f..833291f86 100644 --- a/scala/src/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunction.scala +++ b/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) = { - val referenceSource = new ReferenceDataSource(reference) + private def parseLocs(referenceSource: ReferenceDataSource, intervals: List[String]) = { 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) { diff --git a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala index 4888749e9..2b15780f1 100644 --- a/scala/src/org/broadinstitute/sting/queue/function/QFunction.scala +++ b/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()) - doneOutputs.foreach(_.delete()) - failOutputs.foreach(_.delete()) + outputs.foreach(file => deleteOutput(file)) + doneOutputs.foreach(file => deleteOutput(file)) + failOutputs.foreach(file => deleteOutput(file)) + } + + private def deleteOutput(file: File) = { + if (FileUtils.deleteQuietly(file)) + logger.debug("Deleted " + file) } /** diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala index 41506b825..cbf9f9356 100755 --- a/scala/src/org/broadinstitute/sting/queue/pipeline/BamProcessing.scala +++ b/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 diff --git a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala b/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala index a0fd91351..36f7cd537 100755 --- a/scala/src/org/broadinstitute/sting/queue/pipeline/VariantCalling.scala +++ b/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) diff --git a/scala/test/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunctionUnitTest.scala b/scala/test/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunctionUnitTest.scala index d541f1aa0..2b158cc8f 100644 --- a/scala/test/org/broadinstitute/sting/queue/extensions/gatk/IntervalScatterFunctionUnitTest.scala +++ b/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)