Merge remote-tracking branch 'origin/develop' into develop

bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala

@@ -17,15 +17,16 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.annotations.{ RibosomalRefFlat, AnnotationRefFlat }
+import nl.lumc.sasc.biopet.core.annotations.{ AnnotationRefFlat, RibosomalRefFlat }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.core.summary.SummaryQScript
-import nl.lumc.sasc.biopet.core.{ Reference, BiopetFifoPipe, PipelineCommand, SampleLibraryTag }
+import nl.lumc.sasc.biopet.core.{ BiopetFifoPipe, PipelineCommand, Reference, SampleLibraryTag }
 import nl.lumc.sasc.biopet.extensions.bedtools.{ BedtoolsCoverage, BedtoolsIntersect }
 import nl.lumc.sasc.biopet.extensions.picard._
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsFlagstat
 import nl.lumc.sasc.biopet.pipelines.bammetrics.scripts.CoverageStats
 import nl.lumc.sasc.biopet.extensions.tools.BiopetFlagstat
+import nl.lumc.sasc.biopet.utils.intervals.BedCheck
 import org.broadinstitute.gatk.queue.QScript
 
 class BamMetrics(val root: Configurable) extends QScript
@@ -72,6 +73,8 @@ class BamMetrics(val root: Configurable) extends QScript
   /** executed before script */
   def init(): Unit = {
     inputFiles :+= new InputFile(inputBam)
+    ampliconBedFile.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
+    roiBedFiles.foreach(BedCheck.checkBedFileToReference(_, referenceFasta(), biopetError = true))
   }
 
   /** Script to add jobs */

bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala

@@ -61,9 +61,9 @@ class BamMetricsTest extends TestNGSuite with Matchers {
   def testBamMetrics(rois: Int, amplicon: Boolean, rna: Boolean, wgs: Boolean) = {
     val map = ConfigUtils.mergeMaps(Map("output_dir" -> BamMetricsTest.outputDir, "rna_metrics" -> rna, "wgs_metrics" -> wgs),
       Map(BamMetricsTest.executables.toSeq: _*)) ++
-      (if (amplicon) Map("amplicon_bed" -> "amplicon.bed") else Map()) ++
+      (if (amplicon) Map("amplicon_bed" -> BamMetricsTest.ampliconBed.getAbsolutePath) else Map()) ++
       (if (rna) Map("annotation_refflat" -> "transcripts.refFlat") else Map()) ++
-      Map("regions_of_interest" -> (1 to rois).map("roi_" + _ + ".bed").toList)
+      Map("regions_of_interest" -> (1 to rois).map(BamMetricsTest.roi(_).getAbsolutePath).toList)
     val bammetrics: BamMetrics = initPipeline(map)
 
     bammetrics.inputBam = BamMetricsTest.bam
@@ -94,6 +94,14 @@ object BamMetricsTest {
 
   val bam = new File(outputDir, "input" + File.separator + "bla.bam")
   Files.touch(bam)
+  val ampliconBed = new File(outputDir, "input" + File.separator + "amplicon_bed.bed")
+  Files.touch(ampliconBed)
+
+  def roi(i: Int): File = {
+    val roi = new File(outputDir, "input" + File.separator + s"roi${i}.bed")
+    Files.touch(roi)
+    roi
+  }
 
   private def copyFile(name: String): Unit = {
     val is = getClass.getResourceAsStream("/" + name)

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetFifoPipe.scala

@@ -73,6 +73,8 @@ class BiopetFifoPipe(val root: Configurable,
 
     _pipesJobs :::= commands
     _pipesJobs = _pipesJobs.distinct
+
+    analysisName = commands.map(_.analysisName).mkString("_")
   }
 
   override def beforeCmd(): Unit = {

biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -132,7 +132,7 @@ trait ReportBuilder extends ToolCommand {
     logger.info("Start")
 
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     require(cmdArgs.outputDir.exists(), "Output dir does not exist")
     require(cmdArgs.outputDir.isDirectory, "Output dir is not a directory")

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala

@@ -80,7 +80,7 @@ object AnnotateVcfWithBed extends ToolCommand {
     logger.info("Start")
 
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val fieldType = cmdArgs.fieldType match {
       case "Integer"   => VCFHeaderLineType.Integer

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala

@@ -53,10 +53,7 @@ object BaseCounter extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs: Args = argsParser.parse(args, Args()) match {
-      case Some(x) => x
-      case _       => throw new IllegalArgumentException
-    }
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     //Sets picard logging level
     htsjdk.samtools.util.Log.setGlobalLogLevel(htsjdk.samtools.util.Log.LogLevel.valueOf(logger.getLevel.toString))

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala

@@ -113,7 +113,7 @@ object BastyGenerateFasta extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    cmdArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (cmdArgs.outputVariants != null) {
       writeVariantsOnly()

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala

@@ -47,7 +47,7 @@ object BedToInterval extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val writer = new PrintWriter(commandArgs.outputFile)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala

@@ -39,7 +39,7 @@ object BedtoolsCoverageToCounts extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (!commandArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + commandArgs.input)
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala

@@ -50,7 +50,7 @@ object BiopetFlagstat extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val inputSam = SamReaderFactory.makeDefault.open(commandArgs.inputFile)
     val iterSam = if (commandArgs.region.isEmpty) inputSam.iterator else {

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala

@@ -71,7 +71,7 @@ object CheckAllelesVcfInBam extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     if (commandArgs.bamFiles.size != commandArgs.samples.size)
       logger.warn("Number of samples is different from number of bam files: additional samples or bam files will not be used")

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ExtractAlignedFastq.scala

@@ -242,7 +242,7 @@ object ExtractAlignedFastq extends ToolCommand {
   def parseArgs(args: Array[String]): Args =
     new OptParser()
       .parse(args, Args())
-      .getOrElse(sys.exit(1))
+      .getOrElse(throw new IllegalArgumentException)
 
   def main(args: Array[String]): Unit = {
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala

@@ -45,7 +45,7 @@ object FastqSplitter extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val groupSize = 100
     val output = for (file <- commandArgs.outputFile) yield new AsyncFastqWriter(new BasicFastqWriter(file), groupSize)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSync.scala

@@ -151,7 +151,7 @@ object FastqSync extends ToolCommand {
    */
   def parseArgs(args: Array[String]): Args = new OptParser()
     .parse(args, Args())
-    .getOrElse(sys.exit(1))
+    .getOrElse(throw new IllegalArgumentException)
 
   def main(args: Array[String]): Unit = {
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala

@@ -46,7 +46,7 @@ object FindRepeatsPacBio extends ToolCommand {
   def main(args: Array[String]): Unit = {
 
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
     val bamReader = SamReaderFactory.makeDefault
       .validationStringency(ValidationStringency.SILENT)
       .open(commandArgs.inputBam)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala

@@ -57,7 +57,7 @@ object GvcfToBed extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val cmdArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     logger.debug("Opening reader")
     val reader = new VCFFileReader(cmdArgs.inputVcf, false)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/KrakenReportToJson.scala

@@ -90,7 +90,7 @@ object KrakenReportToJson extends ToolCommand {
    */
   def parseArgs(args: Array[String]): Args = new OptParser()
     .parse(args, Args())
-    .getOrElse(sys.exit(1))
+    .getOrElse(throw new IllegalArgumentException)
 
   /**
    * Takes a line from the kraken report, converts into Map with taxonID and

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala

@@ -50,7 +50,7 @@ object MergeAlleles extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     val readers = commandArgs.inputFiles.map(new VCFFileReader(_, true))
     val referenceFile = new FastaSequenceFile(commandArgs.reference, true)

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala

@@ -41,7 +41,7 @@ object MergeOtuMaps extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     val argsParser = new OptParser
-    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
 
     var map: Map[Long, String] = Map()
 

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeTables.scala

@@ -188,7 +188,7 @@ object MergeTables extends ToolCommand {
   /** Parses the command line argument */
   def parseArgs(args: Array[String]): Args = new OptParser()
     .parse(args, Args())
-    .getOrElse(sys.exit(1))
+    .getOrElse(throw new IllegalArgumentException)
 
   /** Transforms the input file seq into a seq of [[InputTable]] objects */
   def prepInput(inFiles: Seq[File], ext: String, columnNames: Option[Seq[String]]): Seq[InputTable] = {