Fix compile errors

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

@@ -15,21 +15,12 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, PrintWriter }
+import java.io.File
 
-import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
-import htsjdk.samtools.reference.IndexedFastaSequenceFile
-import htsjdk.variant.variantcontext.VariantContext
-import htsjdk.variant.vcf.VCFFileReader
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Reference, ToolCommand, ToolCommandFuntion }
-import nl.lumc.sasc.biopet.utils.VcfUtils._
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.JavaConversions._
-import scala.collection.mutable.ListBuffer
-import scala.collection.parallel.ParMap
-
 class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
   javaMainClass = getClass.getName
 

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

@@ -15,15 +15,12 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, PrintWriter }
+import java.io.File
 
-import htsjdk.samtools.{ SAMSequenceRecord, SamReaderFactory }
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.io.Source
-
 /**
  * @deprecated Use picard.util.BedToIntervalList instead
  */

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

@@ -15,15 +15,12 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, PrintWriter }
+import java.io.File
 
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.{ mutable, SortedMap }
-import scala.io.Source
-
 class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 

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

@@ -15,18 +15,14 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, PrintWriter }
+import java.io.File
 
-import htsjdk.samtools.{ SAMRecord, SamReaderFactory }
-import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.JavaConversions._
-import scala.collection.mutable
-
 class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
   javaMainClass = getClass.getName
 

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

@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**

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

@@ -17,14 +17,11 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
-import nl.lumc.sasc.biopet.utils.config.Configurable
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.core.summary.Summarizable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.annotation.tailrec
-import scala.collection.JavaConverters._
 import scala.io.Source
 import scala.util.matching.Regex
 

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

@@ -17,18 +17,10 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.samtools.reference.FastaSequenceFile
-import htsjdk.variant.variantcontext.{ Allele, VariantContext, VariantContextBuilder }
-import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
-import htsjdk.variant.vcf.{ VCFFileReader, VCFHeader }
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.JavaConversions._
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.{ Map, Set }
-
 class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 

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

@@ -15,14 +15,13 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ BufferedWriter, File, FileWriter, OutputStreamWriter }
+import java.io.File
 
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.collection.mutable.{ Set => MutSet }
-import scala.io.{ BufferedSource, Source }
 
 /**
  * Biopet wrapper for the [[MergeTables]] command line tool.

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

@@ -15,20 +15,16 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, PrintWriter }
+import java.io.File
 
 import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Reference, ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.collection.JavaConversions._
-import scala.collection.mutable
-import scala.collection.mutable.ArrayBuffer
-import scala.io.Source
-import scala.math.{ floor, round }
 
 class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
   javaMainClass = getClass.getName

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

@@ -17,9 +17,8 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.samtools.fastq.{ AsyncFastqWriter, BasicFastqWriter, FastqReader, FastqRecord }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
@@ -51,7 +50,7 @@ class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
     optional("-s", prefixSeq)
 }
 
-object PrefixFastq extends ToolCommand {
+object PrefixFastq {
   /**
    * Create a PrefixFastq class object with a sufix ".prefix.fastq" in the output folder
    *

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

@@ -15,16 +15,12 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, FileReader, PrintWriter }
+import java.io.File
 
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.biojava3.sequencing.io.fastq.{ Fastq, SangerFastqReader, StreamListener }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.Map
-
 class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateLibrary.scala

@@ -15,19 +15,12 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, PrintWriter }
+import java.io.File
 
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
-import org.biojava3.core.sequence.DNASequence
-import org.biojava3.core.sequence.io.FastaReaderHelper
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.JavaConversions._
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.{ Map, Set }
-import scala.util.matching.Regex
-
 class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/SageCreateTagCounts.scala

@@ -15,16 +15,12 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{ File, PrintWriter }
+import java.io.File
 
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ ToolCommand, ToolCommandFuntion }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.{ mutable, SortedMap }
-import scala.collection.mutable.Map
-import scala.io.Source
-
 class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName
 

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

@@ -2,6 +2,12 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.summary.Summarizable
+import nl.lumc.sasc.biopet.utils.ConfigUtils
+import nl.lumc.sasc.biopet.utils.config.Configurable
+import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
+
 /**
  * Seqstat function class for usage in Biopet pipelines
  *

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

@@ -2,9 +2,9 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Created by pjvanthof on 22/08/15.

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

@@ -17,14 +17,9 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
-import htsjdk.variant.variantcontext.{GenotypeType, VariantContext}
-import htsjdk.variant.vcf.VCFFileReader
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
-
-import scala.collection.JavaConversions._
-import scala.io.Source
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
   javaMainClass = getClass.getName

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

@@ -15,23 +15,14 @@
  */
 package nl.lumc.sasc.biopet.tools
 
-import java.io.{File, FileOutputStream, PrintWriter}
-
-import htsjdk.samtools.reference.FastaSequenceFile
-import htsjdk.samtools.util.Interval
-import htsjdk.variant.variantcontext.{Allele, Genotype, VariantContext}
-import htsjdk.variant.vcf.VCFFileReader
-import nl.lumc.sasc.biopet.core.Reference
-import nl.lumc.sasc.biopet.core.summary.{Summarizable, SummaryQScript}
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.summary.{ Summarizable, SummaryQScript }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-import scala.collection.JavaConversions._
-import scala.collection.mutable
 import scala.io.Source
-import scala.sys.process.{Process, ProcessLogger}
-import scala.util.Random
 
 /**
  * This tool will generate statistics from a vcf file

public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/tools/VcfWithVcf.scala

@@ -16,16 +16,10 @@
 package nl.lumc.sasc.biopet.tools
 
 import java.io.File
-import java.util
 
-import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
-import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
-import htsjdk.variant.vcf._
-import nl.lumc.sasc.biopet.utils.VcfUtils.scalaListToJavaObjectArrayList
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
-
-import scala.collection.JavaConversions._
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Biopet extension for tool VcfWithVcf

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

@@ -17,15 +17,9 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import htsjdk.tribble.TribbleException
-import htsjdk.variant.variantcontext.writer.{AsyncVariantContextWriter, VariantContextWriterBuilder}
-import htsjdk.variant.variantcontext.{VariantContext, VariantContextBuilder}
-import htsjdk.variant.vcf._
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
-
-import scala.collection.JavaConversions._
-import scala.collection.mutable.{Map => MMap}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * This tool parses a VEP annotated VCF into a standard VCF file.

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

@@ -17,17 +17,9 @@ package nl.lumc.sasc.biopet.tools
 
 import java.io.File
 
-import com.google.common.hash.{BloomFilter, Funnel}
-import htsjdk.samtools.util.{Interval, IntervalTreeMap}
-import htsjdk.samtools.{QueryInterval, SAMFileWriter, SAMFileWriterFactory, SAMRecord, SamReader, SamReaderFactory, ValidationStringency}
+import nl.lumc.sasc.biopet.core.ToolCommandFuntion
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.utils.intervals.BedRecordList
-import org.apache.commons.io.FilenameUtils.getExtension
-import org.broadinstitute.gatk.utils.commandline.{Input, Output}
-
-import scala.collection.JavaConverters._
-import scala.io.Source
-import scala.math.{max, min}
+import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 // TODO: finish implementation for usage in pipelines
 /**