diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
index 8365cc946ef6395409744f612eec2d9e3b6b52af..eb3a51b54f3d050cbf6c9766e3eef81b1c8607c7 100644
--- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
+++ b/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(throw new IllegalArgumentException)
+ 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")
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
index e80887e8edcb5e8f2c73cfa268964fb39cf326c8..13d579930cc0d5faa0979498a87440f62453b6ba 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala
+++ b/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(throw new IllegalArgumentException)
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val fieldType = cmdArgs.fieldType match {
case "Integer" => VCFHeaderLineType.Integer
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
index 6bba497ca162ca63574fb99f048cba119f9e9cf6..66b8af4b3eab2dcc3d4b6469c7cae27e2c26bc26 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
+++ b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala
@@ -53,7 +53,7 @@ object BaseCounter extends ToolCommand {
def main(args: Array[String]): Unit = {
val argsParser = new OptParser
- val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse(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))
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
index 100209b1d266bd326c91c543631a8b4dfd78c10d..cb482e6706a5f1a4632d75ad9bccff43e1633474 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
+++ b/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(throw new IllegalArgumentException)
+ cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
if (cmdArgs.outputVariants != null) {
writeVariantsOnly()
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
index b82b7b74286258ac5bdd11a796c1924bd1c3d4af..6461d5417aaabe4a8481bdbc9d2c213dba7228a4 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala
+++ b/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(throw new IllegalArgumentException)
+ val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val writer = new PrintWriter(commandArgs.outputFile)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
index 40ad0b93b3ad8404382be17ff8fa862851db961a..c5509721ad6375aefd3f1deb586fb6bfe193528e 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
index 51f1c1cbecba4e079534eaa380f8be072950c3d1..5d53f2ef8ab2be24fff67af1fee6504181dac0e7 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala
+++ b/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(throw new IllegalArgumentException)
+ 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 {
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
index fccebd08aa15ea28c90f6b64af57e196e6091e55..ff7a9036c189fa2f89488ffb8b281537e65e6a6e 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala
+++ b/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(throw new IllegalArgumentException)
+ 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")
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
index f0214b3392255f2c4e81de571c35a152343a86d5..b85a935b1e49b1545bb3dd6ed28c782a98a97be1 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
index 92c8782a75707b646e9cc10e3a97f822a2f53ae0..4daee3d96b843926bf26da0717b69ebe1c176291 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala
+++ b/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(throw new IllegalArgumentException)
+ val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val bamReader = SamReaderFactory.makeDefault
.validationStringency(ValidationStringency.SILENT)
.open(commandArgs.inputBam)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
index fcb302c3c7b9e551d9a7190d14c4d9f29ce48478..bb9e239480906d6390b76644a349440056aca2ec 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala
+++ b/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(throw new IllegalArgumentException)
+ val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
logger.debug("Opening reader")
val reader = new VCFFileReader(cmdArgs.inputVcf, false)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
index 8187064d10ddbfda5a4642a821b30b23e56bfbe4..a64a8e8fd92bf6c35120109fd8be8f22c43ec2e3 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
index f853d66a5018559569a02b5ded85a04e19d57711..4caf55ab0ebdde7f861e8582d32c0715cabf8169 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala
+++ b/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(throw new IllegalArgumentException)
+ val commandArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
var map: Map[Long, String] = Map()
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
index df159c33dd4c05af042ea8f6cfc5a1735cac6013..cb0dbce5a01fc56a0ef0a615327ea5a4ea2972bd 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
index 6be7f11fb878af4e6679f661327f9b85cc3ab4a3..23a981d516fd80ba1d676645b5da268e78d598bf 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
index 4af0fc390709c0e7e5ac7f3fc7e3fdeb0c48e8a1..bb93144eba8fc32e2b076ada8b15542336307af0 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala
+++ b/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(throw new IllegalArgumentException)
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
logger.info("Start")
logger.info("Reading bed file")
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
index 0ea5fcc73ff7f1c5caed520ce8360d1d2c1dd820..66d4f2e1db1bfeadbadd24d30c3a482985455188 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
index 71dfbbacb788829a98821e00fe51d28f47830423..2b0c203e3da70a88dd6ed899772c3d876e93e58f 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
index 2ae201ea18512c2f3ee5a6b7c05efad3015b3cba..58b3976f1534bc744ff732fe5f8befbbb0171150 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
index 4d1f2b82d865cbed58ee329c6f985646df6ed5e3..36ec914e31445381dd8cf4850bbf26727f5f3f16 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
+++ b/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(throw new IllegalArgumentException)
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val jsonString = stringFromInputs(cmdArgs.inputFiles, cmdArgs.tagFiles)
cmdArgs.outputFile match {
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
index 413d335ab01b3897e7d4a2eff2205923cd06fc6b..b6b1780a56249d49700dde42fc62c38ec4540f88 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
index 084a8cf693a0dbb9fd9708dd624df60c3c2629ed..44519d087f20f38fea420ef2b4dba326c6bf0e43 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala
+++ b/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(throw new IllegalArgumentException)
+ val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val summary = new Summary(cmdArgs.summary)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
index 975a6dbd13e4741e93a1709f8f02e01283f216b1..76c55043e4b379d7d9b071895d6f10af69f0ed5c 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala
+++ b/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(throw new IllegalArgumentException)
+ 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)
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 3897c3c9e577e9bb81e0075ba3729b8aa52d7ce3..8833ad596defb0179ed5ad75544afb5a1ea45c44 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/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(throw new IllegalArgumentException)
+ val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val reader = new VCFFileReader(cmdArgs.inputVcf, false)
val header = reader.getFileHeader
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
index 677b4d739621f718b0d4c1d1f9f5531ca465ee7f..09a251ad381fee30896d48e07dc2fe6fb1291045 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
+++ b/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(throw new IllegalArgumentException)
+ cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
val reader = new VCFFileReader(cmdArgs.inputFile, true)
val header = reader.getFileHeader
diff --git a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala b/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
index a86eb7c630f4a605c9f4c96a56f8c8e2ea7e89e0..0a03991ed928d9aa3a9795bdd1f7dbf6526ab2f5 100644
--- a/biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala
+++ b/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(throw new IllegalArgumentException)
+ 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(