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biopet.biopet
Commits
6e7eeb41
Commit
6e7eeb41
authored
Oct 21, 2015
by
Wai Yi Leung
Browse files
Fix typo of trait class ToolCommandFuntion -> ToolCommandFunction #221
parent
7d751299
Changes
22
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFuntion.scala
→
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommandFun
c
tion.scala
View file @
6e7eeb41
...
...
@@ -5,7 +5,7 @@ import nl.lumc.sasc.biopet.FullVersion
/**
* Created by pjvanthof on 11/09/15.
*/
trait
ToolCommandFuntion
extends
BiopetJavaCommandLineFunction
with
Version
{
trait
ToolCommandFun
c
tion
extends
BiopetJavaCommandLineFunction
with
Version
{
def
toolObject
:
Object
def
versionCommand
=
""
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
/** Report builder object */
val
builder
:
ReportBuilder
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/BastyGenerateFasta.scala
View file @
6e7eeb41
...
...
@@ -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
,
ToolCommandFun
c
tion
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Reference
{
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
ToolCommandFun
c
tion
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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
,
ToolCommandFun
c
tion
}
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
ToolCommandFun
c
tion
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MergeTables
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
View file @
6e7eeb41
...
...
@@ -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
,
ToolCommandFun
c
tion
}
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
ToolCommandFun
c
tion
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
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
View file @
6e7eeb41
...
...
@@ -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
,
ToolCommandFun
c
tion
}
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
ToolCommandFun
c
tion
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
View file @
6e7eeb41
...
...
@@ -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.ToolCommandFun
c
tion
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
ToolCommandFun
c
tion
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfWithVcf
@Input
(
doc
=
"Input vcf file"
,
shortName
=
"input"
,
required
=
true
)
...
...
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