Merge branch 'fix-exit_calls' into 'develop'

Changes arg parser with getOrElse(throw new IllegalArgumentException)

Fixes #342 

See merge request !402

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] = {

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

@@ -62,7 +62,7 @@ object MpileupToVcf 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 != null && !commandArgs.input.exists) throw new IllegalStateException("Input file does not exist")
 
     val writer = new PrintWriter(commandArgs.output)

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

@@ -52,7 +52,7 @@ object PrefixFastq 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 writer = new AsyncFastqWriter(new BasicFastqWriter(cmdArgs.output), 3000)
     val reader = new FastqReader(cmdArgs.input)

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

@@ -49,7 +49,7 @@ object RegionAfCount extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     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)
 
     logger.info("Start")
     logger.info("Reading bed file")

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

@@ -41,7 +41,7 @@ object SageCountFastq 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/SageCreateLibrary.scala

@@ -74,7 +74,7 @@ object SageCreateLibrary 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/SageCreateTagCounts.scala

@@ -52,7 +52,7 @@ object SageCreateTagCounts 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/SamplesTsvToJson.scala

@@ -46,7 +46,7 @@ object SamplesTsvToJson extends ToolCommand {
   /** Executes SamplesTsvToJson */
   def main(args: Array[String]): Unit = {
     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 jsonString = stringFromInputs(cmdArgs.inputFiles, cmdArgs.tagFiles)
     cmdArgs.outputFile match {

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

@@ -76,7 +76,7 @@ object SeqStat extends ToolCommand {
    */
   def parseArgs(args: Array[String]): Args = new OptParser()
     .parse(args, Args())
-    .getOrElse(sys.exit(1))
+    .getOrElse(throw new IllegalArgumentException)
 
   /**
    *

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

@@ -46,7 +46,7 @@ object SquishBed extends ToolCommand {
    */
   def main(args: Array[String]): Unit = {
     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)
 
     if (!cmdArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + cmdArgs.input)
 

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

@@ -61,7 +61,7 @@ object SummaryToTsv extends ToolCommand {
 
   def main(args: Array[String]): Unit = {
     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 summary = new Summary(cmdArgs.summary)
 

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

@@ -51,7 +51,7 @@ object ValidateFastq extends ToolCommand {
 
     //parse all possible options into OptParser
     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)
 
     //read in fastq file 1 and if present fastq file 2
     val readFq1 = new FastqReader(cmdArgs.input)

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

@@ -137,7 +137,7 @@ object VcfFilter extends ToolCommand {
   def main(args: Array[String]): Unit = {
     logger.info("Start")
     val argsParser = new OptParser
-    val cmdArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    val cmdArgs = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
 
     val reader = new VCFFileReader(cmdArgs.inputVcf, false)
     val header = reader.getFileHeader

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

@@ -206,7 +206,7 @@ object VcfStats extends ToolCommand {
   def main(args: Array[String]): Unit = {
     logger.info("Started")
     val argsParser = new OptParser
-    cmdArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+    cmdArgs = argsParser.parse(args, Args()) getOrElse(throw new IllegalArgumentException)
 
     val reader = new VCFFileReader(cmdArgs.inputFile, true)
     val header = reader.getFileHeader

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

@@ -72,7 +72,7 @@ object VcfToTsv 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)
 
     // Throw exception if separator and listSeparator are identical
     if (commandArgs.separator == commandArgs.listSeparator) throw new IllegalArgumentException(

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

@@ -39,7 +39,7 @@ object VepNormalizer extends ToolCommand {
   def main(args: Array[String]): Unit = {
     val commandArgs: Args = new OptParser()
       .parse(args, Args())
-      .getOrElse(sys.exit(1))
+      .getOrElse(throw new IllegalArgumentException)
 
     val input = commandArgs.inputVCF
     val output = commandArgs.outputVCF

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

@@ -399,7 +399,7 @@ object WipeReads 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)
 
   def main(args: Array[String]): Unit = {