Merge branch 'fix-typo-toolcommandfuntion' into 'develop'

Fix typo of trait class ToolCommandFuntion -> ToolCommandFunction #221

Fixes #221 

See merge request !258

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala → public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFunction.scala

@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.FullVersion
 /**
  * Created by pjvanthof on 11/09/15.
  */
-trait ToolCommandFuntion extends BiopetJavaCommandLineFunction with Version {
+trait ToolCommandFunction extends BiopetJavaCommandLineFunction with Version {
   def toolObject: Object
 
   def versionCommand = ""

public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala

@@ -16,7 +16,7 @@
 package nl.lumc.sasc.biopet.core.report
 
 import java.io._
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.summary.Summary
 import nl.lumc.sasc.biopet.utils.{ ToolCommand, Logging, IoUtils }
 import org.broadinstitute.gatk.utils.commandline.Input
@@ -28,7 +28,7 @@ import scala.collection.mutable
  *
  * @author pjvan_thof
  */
-trait ReportBuilderExtension extends ToolCommandFuntion {
+trait ReportBuilderExtension extends ToolCommandFunction {
 
   /** Report builder object */
   val builder: ReportBuilder

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

@@ -18,10 +18,10 @@ package nl.lumc.sasc.biopet.extensions.tools
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion with Reference {
+class BastyGenerateFasta(val root: Configurable) extends ToolCommandFunction with Reference {
   def toolObject = nl.lumc.sasc.biopet.tools.BastyGenerateFasta
 
   @Input(doc = "Input vcf file", required = false)

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

@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * @deprecated Use picard.util.BedToIntervalList instead
  */
-class BedToInterval(val root: Configurable) extends ToolCommandFuntion {
+class BedToInterval(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.BedToInterval
 
   @Input(doc = "Input Bed file", required = true)

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

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFuntion {
+class BedtoolsCoverageToCounts(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.BedtoolsCoverageToCounts
 
   @Input(doc = "Input fasta", shortName = "input", required = true)

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

@@ -17,13 +17,13 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 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.{ Input, Output }
 
-class BiopetFlagstat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+class BiopetFlagstat(val root: Configurable) extends ToolCommandFunction with Summarizable {
   def toolObject = nl.lumc.sasc.biopet.tools.BiopetFlagstat
 
   @Input(doc = "Input bam", shortName = "input", required = true)

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

@@ -18,14 +18,14 @@ package nl.lumc.sasc.biopet.extensions.tools
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Queue extension for the FastqSplitter
  * @param root Parent object
  */
-class FastqSplitter(val root: Configurable) extends ToolCommandFuntion {
+class FastqSplitter(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.FastqSplitter
 
   @Input(doc = "Input fastq", shortName = "input", required = true)

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, ToolCommandFunction }
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
@@ -30,7 +30,7 @@ import scala.util.matching.Regex
  *
  * @param root Configuration object for the pipeline
  */
-class FastqSync(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+class FastqSync(val root: Configurable) extends ToolCommandFunction with Summarizable {
 
   def toolObject = nl.lumc.sasc.biopet.tools.FastqSync
 

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

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class MergeAlleles(val root: Configurable) extends ToolCommandFuntion {
+class MergeAlleles(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.MergeAlleles
 
   @Input(doc = "Input vcf files", shortName = "input", required = true)

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

@@ -17,7 +17,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -28,7 +28,7 @@ import scala.collection.mutable.{ Set => MutSet }
  *
  * @param root [[Configurable]] object
  */
-class MergeTables(val root: Configurable) extends ToolCommandFuntion {
+class MergeTables(val root: Configurable) extends ToolCommandFunction {
 
   def toolObject = nl.lumc.sasc.biopet.tools.MergeTables
 

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 import java.io.File
 
 import htsjdk.samtools.SamReaderFactory
-import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFuntion }
+import nl.lumc.sasc.biopet.core.{ Reference, ToolCommandFunction }
 import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 import scala.collection.JavaConversions._
 
-class MpileupToVcf(val root: Configurable) extends ToolCommandFuntion with Reference {
+class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Reference {
   def toolObject = nl.lumc.sasc.biopet.tools.MpileupToVcf
 
   @Input(doc = "Input mpileup file", shortName = "mpileup", required = false)

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 import java.io.File
 
 import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
 
 /**
@@ -26,7 +26,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Argument, Input, Output }
  *
  * Created by pjvan_thof on 1/13/15.
  */
-class PrefixFastq(val root: Configurable) extends ToolCommandFuntion {
+class PrefixFastq(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.PrefixFastq
 
   override def defaultCoreMemory = 1.0

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

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class SageCountFastq(val root: Configurable) extends ToolCommandFuntion {
+class SageCountFastq(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.SageCountFastq
 
   @Input(doc = "Input fasta", shortName = "input", required = true)

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

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class SageCreateLibrary(val root: Configurable) extends ToolCommandFuntion {
+class SageCreateLibrary(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.SageCreateLibrary
 
   @Input(doc = "Input fasta", shortName = "input", required = true)

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

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class SageCreateTagCounts(val root: Configurable) extends ToolCommandFuntion {
+class SageCreateTagCounts(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.SageCreateTagCounts
 
   @Input(doc = "Raw count file", shortName = "input", required = true)

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

@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.core.summary.Summarizable
 import nl.lumc.sasc.biopet.utils.ConfigUtils
 import nl.lumc.sasc.biopet.utils.config.Configurable
@@ -13,7 +13,7 @@ import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
  *
  * @param root Configuration object for the pipeline
  */
-class SeqStat(val root: Configurable) extends ToolCommandFuntion with Summarizable {
+class SeqStat(val root: Configurable) extends ToolCommandFunction with Summarizable {
   def toolObject = nl.lumc.sasc.biopet.tools.SeqStat
 
   @Input(doc = "Input FASTQ", shortName = "input", required = true)

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

@@ -2,14 +2,14 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Created by pjvanthof on 22/08/15.
  */
-class SquishBed(val root: Configurable) extends ToolCommandFuntion {
+class SquishBed(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.SquishBed
 
   @Input(doc = "Input Bed file", required = true)

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

@@ -17,11 +17,11 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
-class VcfFilter(val root: Configurable) extends ToolCommandFuntion {
+class VcfFilter(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.VcfFilter
 
   @Input(doc = "Input vcf", shortName = "I", required = true)

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

@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.tools
 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.core.{ Reference, ToolCommandFunction }
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
@@ -29,7 +29,7 @@ import scala.io.Source
  *
  * Created by pjvan_thof on 1/10/15.
  */
-class VcfStats(val root: Configurable) extends ToolCommandFuntion with Summarizable with Reference {
+class VcfStats(val root: Configurable) extends ToolCommandFunction with Summarizable with Reference {
   def toolObject = nl.lumc.sasc.biopet.tools.VcfStats
 
   @Input(doc = "Input fastq", shortName = "I", required = true)

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

@@ -17,14 +17,14 @@ package nl.lumc.sasc.biopet.extensions.tools
 
 import java.io.File
 
-import nl.lumc.sasc.biopet.core.ToolCommandFuntion
+import nl.lumc.sasc.biopet.core.ToolCommandFunction
 import nl.lumc.sasc.biopet.utils.config.Configurable
 import org.broadinstitute.gatk.utils.commandline.{ Input, Output }
 
 /**
  * Biopet extension for tool VcfWithVcf
  */
-class VcfWithVcf(val root: Configurable) extends ToolCommandFuntion {
+class VcfWithVcf(val root: Configurable) extends ToolCommandFunction {
   def toolObject = nl.lumc.sasc.biopet.tools.VcfWithVcf
 
   @Input(doc = "Input vcf file", shortName = "input", required = true)