From 80de022e0c85bf386dcdc5e349a27de1e71e5b1c Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 17 May 2016 11:43:39 +0200
Subject: [PATCH] Style changes
---
.../nl/lumc/sasc/biopet/core/report/ReportBuilder.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/AnnotateVcfWithBed.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/BaseCounter.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/BedToInterval.scala | 2 +-
.../lumc/sasc/biopet/tools/BedtoolsCoverageToCounts.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/BiopetFlagstat.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBam.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/FastqSplitter.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/FindRepeatsPacBio.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/GvcfToBed.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/MergeAlleles.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/MergeOtuMaps.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/PrefixFastq.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/RegionAfCount.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/SageCountFastq.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala | 2 +-
.../nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/SquishBed.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/SummaryToTsv.scala | 2 +-
.../scala/nl/lumc/sasc/biopet/tools/ValidateFastq.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala | 2 +-
.../main/scala/nl/lumc/sasc/biopet/tools/VcfToTsv.scala | 2 +-
.../biopet/pipelines/generateindexes/WriteConfig.scala | 8 ++++----
27 files changed, 30 insertions(+), 30 deletions(-)
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 8365cc946..eb3a51b54 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 e80887e8e..13d579930 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 6bba497ca..66b8af4b3 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 100209b1d..cb482e670 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 b82b7b742..6461d5417 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 40ad0b93b..c5509721a 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 51f1c1cbe..5d53f2ef8 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 fccebd08a..ff7a9036c 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 f0214b339..b85a935b1 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 92c8782a7..4daee3d96 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 fcb302c3c..bb9e23948 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 8187064d1..a64a8e8fd 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 f853d66a5..4caf55ab0 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 df159c33d..cb0dbce5a 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 6be7f11fb..23a981d51 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 4af0fc390..bb93144eb 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 0ea5fcc73..66d4f2e1d 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 71dfbbacb..2b0c203e3 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 2ae201ea1..58b3976f1 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 4d1f2b82d..36ec914e3 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 413d335ab..b6b1780a5 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 084a8cf69..44519d087 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 975a6dbd1..76c55043e 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 3897c3c9e..8833ad596 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 677b4d739..09a251ad3 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 a86eb7c63..0a03991ed 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(
diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfig.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfig.scala
index c087725b6..ce14261e0 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfig.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/generateindexes/WriteConfig.scala
@@ -1,14 +1,14 @@
package nl.lumc.sasc.biopet.pipelines.generateindexes
-import java.io.{File, PrintWriter}
+import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import org.broadinstitute.gatk.queue.function.InProcessFunction
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
/**
- * Created by pjvanthof on 15/05/16.
- */
+ * Created by pjvanthof on 15/05/16.
+ */
class WriteConfig extends InProcessFunction {
@Input
var deps: List[File] = Nil
--
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