Commit 6e7eeb41 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix typo of trait class ToolCommandFuntion -> ToolCommandFunction #221

parent 7d751299
......@@ -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 = ""
......
......@@ -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
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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
......
......@@ -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)
......
......@@ -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
......
......@@ -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)
......
......@@ -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
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
......@@ -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)
......
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