Code style fixes

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala

@@ -19,7 +19,7 @@ import java.io.File
 
 import nl.lumc.sasc.biopet.core.config.Configurable
 import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Extension for en general line plot with R

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

@@ -15,20 +15,20 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{PrintWriter, InputStream, File}
+import java.io.{ PrintWriter, InputStream, File }
 import java.util
 
 import htsjdk.samtools.util.Interval
-import htsjdk.samtools.{QueryInterval, SAMRecord, SamReader, SamReaderFactory}
+import htsjdk.samtools.{ QueryInterval, SAMRecord, SamReader, SamReaderFactory }
 import htsjdk.tribble.AbstractFeatureReader._
-import htsjdk.tribble.{AbstractFeatureReader, TabixFeatureReader}
-import htsjdk.tribble.bed.{BEDFeature, SimpleBEDFeature, BEDCodec, FullBEDFeature}
-import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
-import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
-import htsjdk.variant.vcf.{VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine}
+import htsjdk.tribble.{ AbstractFeatureReader, TabixFeatureReader }
+import htsjdk.tribble.bed.{ BEDFeature, SimpleBEDFeature, BEDCodec, FullBEDFeature }
+import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
+import htsjdk.variant.variantcontext.{ VariantContext, VariantContextBuilder }
+import htsjdk.variant.vcf.{ VCFFileReader, VCFHeaderLineCount, VCFHeaderLineType, VCFInfoHeaderLine }
 import nl.lumc.sasc.biopet.core.ToolCommand
 import nl.lumc.sasc.biopet.extensions.rscript.ScatterPlot
-import nl.lumc.sasc.biopet.utils.intervals.{BedRecord, BedRecordList}
+import nl.lumc.sasc.biopet.utils.intervals.{ BedRecord, BedRecordList }
 
 import scala.collection.JavaConversions._
 import scala.collection.JavaConverters._
@@ -54,10 +54,10 @@ object RegionAfCount extends ToolCommand {
       c.copy(scatterpPlot = Some(x))
     }
     opt[File]('V', "vcfFile") unbounded () minOccurs 1 action { (x, c) =>
-      c.copy(vcfFiles = c.vcfFiles ::: x :: Nil )
+      c.copy(vcfFiles = c.vcfFiles ::: x :: Nil)
     }
     opt[Unit]("exonsOnly") unbounded () action { (x, c) =>
-      c.copy(exonsOnly = true )
+      c.copy(exonsOnly = true)
     }
   }
 
@@ -87,7 +87,7 @@ object RegionAfCount extends ToolCommand {
         for (variant <- it) {
           val sum = (variant.getAttribute("AF", 0) match {
             case a: util.ArrayList[_] => a.map(_.toString.toDouble).toArray
-            case s => Array(s.toString.toDouble)
+            case s                    => Array(s.toString.toDouble)
           }).sum
           bedRecords
             .overlapWith(BedRecord(variant.getContig, variant.getStart, variant.getEnd))

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

+package nl.lumc.sasc.biopet.tools
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.ToolCommand
+import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
+
+/**
+ * Created by pjvanthof on 22/08/15.
+ */
+object SquishBed extends ToolCommand {
+
+  case class Args(input: File = null, output: File = null) extends AbstractArgs
+
+  class OptParser extends AbstractOptParser {
+    opt[File]('I', "input") required () valueName "<file>" action { (x, c) =>
+      c.copy(input = x)
+    }
+    opt[File]('o', "output") required () unbounded () valueName "<file>" action { (x, c) =>
+      c.copy(output = x)
+    }
+  }
+
+  /**
+   * @param args the command line arguments
+   */
+  def main(args: Array[String]): Unit = {
+    val argsParser = new OptParser
+    val cmdArgs: Args = argsParser.parse(args, Args()) getOrElse sys.exit(1)
+
+    if (!cmdArgs.input.exists) throw new IllegalStateException("Input file not found, file: " + cmdArgs.input)
+
+    val records = BedRecordList.fromFile(cmdArgs.input).squishBed()
+
+  }
+}

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/intervals/BedRecord.scala

@@ -24,7 +24,7 @@ case class BedRecord(chr: String,
     Some(BedRecordList.fromList(for (i <- 0 to blockCount.get) yield {
       val exonNumber = strand match {
         case Some(false) => blockCount.get - i
-        case _ => i + 1
+        case _           => i + 1
       }
       val record = BedRecord(chr, start + blockStarts(i), start + blockStarts(i) + blockSizes(i),
         name.map(_ + s"_exon-$exonNumber"))
@@ -37,7 +37,7 @@ case class BedRecord(chr: String,
     Some(BedRecordList.fromList(for (i <- 0 to (blockCount.get - 1)) yield {
       val intronNumber = strand match {
         case Some(false) => blockCount.get - i
-        case _ => i + 1
+        case _           => i + 1
       }
       val record = BedRecord(chr, start + start + blockStarts(i) + blockSizes(i) + 1, start + blockStarts(i + 1) - 1,
         name.map(_ + s"_intron-$intronNumber"))
@@ -65,11 +65,11 @@ object BedRecord {
       values.lift(5).map(_ match {
         case "-" => false
         case "+" => true
-        case _ => throw new IllegalStateException("Strand (column 6) must be '+' or '-'")
+        case _   => throw new IllegalStateException("Strand (column 6) must be '+' or '-'")
       }),
       values.lift(6).map(_.toInt),
-      values.lift(7)map(_.toInt),
-      values.lift(8).map(_.split(",", 3).map(_.toInt)).map(x => (x.lift(0).getOrElse(0),x.lift(1).getOrElse(0),x.lift(2).getOrElse(0))),
+      values.lift(7) map (_.toInt),
+      values.lift(8).map(_.split(",", 3).map(_.toInt)).map(x => (x.lift(0).getOrElse(0), x.lift(1).getOrElse(0), x.lift(2).getOrElse(0))),
       values.lift(9).map(_.toInt),
       values.lift(10).map(_.split(",").map(_.toInt)).getOrElse(Array()),
       values.lift(11).map(_.split(",").map(_.toInt)).getOrElse(Array())