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biopet.biopet
Commits
19f7d266
Commit
19f7d266
authored
May 10, 2016
by
Peter van 't Hof
Browse files
Style fixes
parent
f88088e3
Changes
8
Hide whitespace changes
Inline
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Cnmops.scala
View file @
19f7d266
...
...
@@ -19,7 +19,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Wrapper for the Cnmops command line tool.
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeC.scala
View file @
19f7d266
...
...
@@ -15,9 +15,9 @@
*/
package
nl.lumc.sasc.biopet.extensions.freec
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline._
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCAssessSignificancePlot.scala
View file @
19f7d266
...
...
@@ -4,7 +4,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
FreeCAssessSignificancePlot
(
val
root
:
Configurable
)
extends
RscriptCommandLineFunction
{
protected
var
script
:
File
=
new
File
(
"/nl/lumc/sasc/biopet/extensions/freec/freec_assess_significance.R"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCBAFPlot.scala
View file @
19f7d266
...
...
@@ -4,7 +4,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
FreeCBAFPlot
(
val
root
:
Configurable
)
extends
RscriptCommandLineFunction
{
protected
var
script
:
File
=
new
File
(
"/nl/lumc/sasc/biopet/extensions/freec/freec_BAFPlot.R"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/freec/FreeCCNVPlot.scala
View file @
19f7d266
...
...
@@ -4,7 +4,7 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.extensions.RscriptCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
FreeCCNVPlot
(
val
root
:
Configurable
)
extends
RscriptCommandLineFunction
{
protected
var
script
:
File
=
new
File
(
"/nl/lumc/sasc/biopet/extensions/freec/freec_CNVPlot.R"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMpileup.scala
View file @
19f7d266
...
...
@@ -18,7 +18,7 @@ package nl.lumc.sasc.biopet.extensions.sambamba
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
class
SambambaMpileup
(
val
root
:
Configurable
)
extends
Sambamba
{
override
val
defaultThreads
=
4
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/CnvMethod.scala
View file @
19f7d266
...
...
@@ -5,8 +5,8 @@ import nl.lumc.sasc.biopet.core.Reference
import
org.broadinstitute.gatk.queue.QScript
/**
* Created by pjvanthof on 10/05/16.
*/
* Created by pjvanthof on 10/05/16.
*/
trait
CnvMethod
extends
QScript
with
SummaryQScript
with
Reference
{
/** Name of mode, this should also be used in the config */
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/FreecMethod.scala
View file @
19f7d266
...
...
@@ -2,51 +2,52 @@ package nl.lumc.sasc.biopet.pipelines.kopisu.methods
import
java.io.File
import
nl.lumc.sasc.biopet.extensions.freec.
{
FreeC
,
FreeCAssessSignificancePlot
,
FreeCBAFPlot
,
FreeCCNVPlot
}
import
nl.lumc.sasc.biopet.extensions.freec.
{
FreeC
,
FreeCAssessSignificancePlot
,
FreeCBAFPlot
,
FreeCCNVPlot
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by pjvanthof on 10/05/16.
*/
* Created by pjvanthof on 10/05/16.
*/
class
FreecMethod
(
val
root
:
Configurable
)
extends
CnvMethod
{
def
name
=
"freec"
var
snpFile
:
Option
[
File
]
=
config
(
"snp_file"
,
freeVar
=
false
)
def
biopetScript
:
Unit
=
{
inputBams
.
foreach
{
case
(
sampleName
,
bamFile
)
=>
inputBams
.
foreach
{
case
(
sampleName
,
bamFile
)
=>
val
sampleOutput
=
new
File
(
outputDir
,
sampleName
)
val
sampleOutput
=
new
File
(
outputDir
,
sampleName
)
val
freec
=
new
FreeC
(
this
)
freec
.
input
=
bamFile
freec
.
inputFormat
=
Some
(
"BAM"
)
freec
.
outputPath
=
sampleOutput
freec
.
snpFile
=
snpFile
add
(
freec
)
val
freec
=
new
FreeC
(
this
)
freec
.
input
=
bamFile
freec
.
inputFormat
=
Some
(
"BAM"
)
freec
.
outputPath
=
sampleOutput
freec
.
snpFile
=
snpFile
add
(
freec
)
/*
/*
* These scripts will wait for FreeC to Finish
*
* R-scripts to plot FreeC results
* */
val
fcAssessSignificancePlot
=
new
FreeCAssessSignificancePlot
(
this
)
fcAssessSignificancePlot
.
cnv
=
freec
.
cnvOutput
fcAssessSignificancePlot
.
ratios
=
freec
.
ratioOutput
fcAssessSignificancePlot
.
output
=
new
File
(
sampleOutput
,
sampleName
+
".freec_significant_calls.txt"
)
add
(
fcAssessSignificancePlot
)
val
fcCnvPlot
=
new
FreeCCNVPlot
(
this
)
fcCnvPlot
.
input
=
freec
.
ratioOutput
fcCnvPlot
.
output
=
new
File
(
sampleOutput
,
sampleName
+
".freec_cnv"
)
add
(
fcCnvPlot
)
snpFile
.
foreach
{
_
=>
val
fcBAFPlot
=
new
FreeCBAFPlot
(
this
)
fcBAFPlot
.
input
=
freec
.
bafOutput
fcBAFPlot
.
output
=
new
File
(
sampleOutput
,
sampleName
+
".freec_baf"
)
add
(
fcBAFPlot
)
}
val
fcAssessSignificancePlot
=
new
FreeCAssessSignificancePlot
(
this
)
fcAssessSignificancePlot
.
cnv
=
freec
.
cnvOutput
fcAssessSignificancePlot
.
ratios
=
freec
.
ratioOutput
fcAssessSignificancePlot
.
output
=
new
File
(
sampleOutput
,
sampleName
+
".freec_significant_calls.txt"
)
add
(
fcAssessSignificancePlot
)
val
fcCnvPlot
=
new
FreeCCNVPlot
(
this
)
fcCnvPlot
.
input
=
freec
.
ratioOutput
fcCnvPlot
.
output
=
new
File
(
sampleOutput
,
sampleName
+
".freec_cnv"
)
add
(
fcCnvPlot
)
snpFile
.
foreach
{
_
=>
val
fcBAFPlot
=
new
FreeCBAFPlot
(
this
)
fcBAFPlot
.
input
=
freec
.
bafOutput
fcBAFPlot
.
output
=
new
File
(
sampleOutput
,
sampleName
+
".freec_baf"
)
add
(
fcBAFPlot
)
}
}
}
...
...
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