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biopet.biopet
Commits
2c323f38
Commit
2c323f38
authored
Jul 03, 2015
by
Peter van 't Hof
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Fix code style warnings
parent
7778c07d
Changes
80
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80 changed files
with
339 additions
and
354 deletions
+339
-354
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
...sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
...asc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
+3
-3
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
.../sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
+2
-2
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
...lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
...c/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
.../lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
+3
-3
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
...umc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
...c/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
+2
-2
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
...mc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
...l/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
...biopet/extensions/gatk/broad/RealignerTargetCreator.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
...mc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
.../sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
+2
-2
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
.../sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
+1
-1
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
.../lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
+6
-6
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
...sc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
+1
-1
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
+2
-0
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
.../sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
+3
-3
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
...a/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
+2
-2
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
...ala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
+17
-17
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
...sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
+8
-8
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
.../lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
+3
-3
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
...main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
+8
-7
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
...lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
+2
-0
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
.../scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
+7
-5
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
.../sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
+2
-0
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
...a/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
+2
-0
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
...c/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
+3
-1
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+9
-10
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+21
-21
public/bammetrics/src/test/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
...umc/sasc/biopet/pipelines/bammetrics/BamMetricsTest.scala
+2
-0
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
+2
-0
public/basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/basty/BastyTrait.scala
+4
-4
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
...st/scala/nl/lumc/sasc/biopet/core/config/ConfigTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
...ala/nl/lumc/sasc/biopet/core/config/ConfigValueTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
...la/nl/lumc/sasc/biopet/core/config/ConfigurableTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectAlignmentSummaryMetricsTest.scala
...xtensions/picard/CollectAlignmentSummaryMetricsTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/CollectInsertSizeMetricsTest.scala
...opet/extensions/picard/CollectInsertSizeMetricsTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
...mc/sasc/biopet/extensions/picard/MarkDuplicatesTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
...la/nl/lumc/sasc/biopet/tools/AnnotateVcfWithBedTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
.../nl/lumc/sasc/biopet/tools/CheckAllelesVcfInBamTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
...st/scala/nl/lumc/sasc/biopet/tools/MergeAllelesTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
.../test/scala/nl/lumc/sasc/biopet/tools/VcfFilterTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
...c/test/scala/nl/lumc/sasc/biopet/tools/VcfToTsvTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
...test/scala/nl/lumc/sasc/biopet/tools/VcfWithVcfTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
...est/scala/nl/lumc/sasc/biopet/utils/ConfigUtilsTest.scala
+2
-0
public/biopet-framework/src/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
...rc/test/scala/nl/lumc/sasc/biopet/utils/PackageTest.scala
+2
-0
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+3
-3
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
...scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
+4
-3
public/carp/src/test/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
...t/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpTest.scala
+7
-5
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
...la/nl/lumc/sasc/biopet/pipelines/flexiprep/Cutadapt.scala
+3
-3
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
...cala/nl/lumc/sasc/biopet/pipelines/flexiprep/Fastqc.scala
+9
-9
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
...a/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
+18
-52
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+6
-5
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
...la/nl/lumc/sasc/biopet/pipelines/flexiprep/SeqtkSeq.scala
+11
-11
public/flexiprep/src/test/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
.../lumc/sasc/biopet/pipelines/flexiprep/FlexiprepTest.scala
+5
-3
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala
+19
-23
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
...scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+4
-4
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
...nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
+4
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
...c/biopet/pipelines/gentrap/extensions/CustomVarScan.scala
+3
-3
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RScriptCommandLineFunction.scala
...lines/gentrap/extensions/RScriptCommandLineFunction.scala
+0
-0
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
.../biopet/pipelines/gentrap/extensions/RawBaseCounter.scala
+1
-1
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
...sasc/biopet/pipelines/gentrap/scripts/AggrBaseCount.scala
+1
-1
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
...l/lumc/sasc/biopet/pipelines/kopisu/ConiferPipeline.scala
+2
-2
public/kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
...nl/lumc/sasc/biopet/pipelines/kopisu/ConiferSummary.scala
+5
-3
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
...scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+24
-71
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
...nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
+4
-3
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/scripts/TophatRecondition.scala
.../biopet/pipelines/mapping/scripts/TophatRecondition.scala
+1
-1
public/mapping/src/test/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
...a/nl/lumc/sasc/biopet/pipelines/mapping/MappingTest.scala
+5
-3
public/sage/src/main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
.../main/scala/nl/lumc/sasc/biopet/pipelines/sage/Sage.scala
+4
-4
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+2
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+3
-3
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
...cala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+9
-9
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
...umc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
+2
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
...asc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
+11
-9
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
...scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTest.scala
+6
-4
public/shiva/src/test/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
...sasc/biopet/pipelines/shiva/ShivaVariantcallingTest.scala
+2
-0
public/toucan/src/main/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/toucan/Toucan.scala
+2
-0
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
...n/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
+4
-4
No files found.
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/AnalyzeCovariates.scala
View file @
2c323f38
...
...
@@ -18,6 +18,6 @@ object AnalyzeCovariates {
ac
.
before
=
before
ac
.
after
=
after
ac
.
plots
=
plots
return
ac
ac
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/ApplyRecalibration.scala
View file @
2c323f38
...
...
@@ -12,8 +12,8 @@ import nl.lumc.sasc.biopet.core.config.Configurable
class
ApplyRecalibration
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
ApplyRecalibration
with
GatkGeneral
{
scatterCount
=
config
(
"scattercount"
,
default
=
0
)
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
nt
=
Option
(
getThreads
(
3
))
memoryLimit
=
Option
(
nt
.
getOrElse
(
1
)
*
2
)
...
...
@@ -37,6 +37,6 @@ object ApplyRecalibration {
ar
.
recal_file
=
recal_file
ar
.
tranches_file
=
tranches_file
ar
.
out
=
output
return
ar
ar
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/BaseRecalibrator.scala
View file @
2c323f38
...
...
@@ -20,7 +20,7 @@ object BaseRecalibrator {
val
br
=
new
BaseRecalibrator
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
br
.
beforeGraph
return
br
br
.
beforeGraph
()
br
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineGVCFs.scala
View file @
2c323f38
...
...
@@ -18,6 +18,6 @@ object CombineGVCFs {
val
cg
=
new
CombineGVCFs
(
root
)
cg
.
variant
=
input
cg
.
o
=
output
return
cg
cg
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/CombineVariants.scala
View file @
2c323f38
...
...
@@ -18,6 +18,6 @@ object CombineVariants {
val
cv
=
new
CombineVariants
(
root
)
cv
.
variant
=
input
cv
.
out
=
output
return
cv
cv
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
View file @
2c323f38
...
...
@@ -26,10 +26,10 @@ trait GatkGeneral extends CommandLineGATK with BiopetJavaCommandLineFunction wit
override
val
versionExitcode
=
List
(
0
,
1
)
override
def
versionCommand
=
executable
+
" -jar "
+
jarFile
+
" -version"
override
def
getVersion
=
super
.
getVersion
.
collect
{
case
v
ersion
=>
"Gatk "
+
version
}
override
def
getVersion
=
super
.
getVersion
.
collect
{
case
v
=>
"Gatk "
+
v
}
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
reference_sequence
==
null
)
reference_sequence
=
referenceFasta
()
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
2c323f38
...
...
@@ -29,6 +29,6 @@ object GenotypeGVCFs {
val
gg
=
new
GenotypeGVCFs
(
root
)
gg
.
variant
=
gvcfFiles
gg
.
out
=
output
return
gg
gg
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
2c323f38
...
...
@@ -35,8 +35,8 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
bamOutput
!=
null
&&
nct
.
getOrElse
(
1
)
>
1
)
{
threads
=
1
logger
.
warn
(
"BamOutput is on, nct/threads is forced to set on 1, this option is only for debug"
)
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/IndelRealigner.scala
View file @
2c323f38
...
...
@@ -19,6 +19,6 @@ object IndelRealigner {
ir
.
input_file
:+=
input
ir
.
targetIntervals
=
targetIntervals
ir
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.bam"
)
return
ir
ir
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/PrintReads.scala
View file @
2c323f38
...
...
@@ -18,6 +18,6 @@ object PrintReads {
val
br
=
new
PrintReads
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
return
br
br
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/RealignerTargetCreator.scala
View file @
2c323f38
...
...
@@ -20,6 +20,6 @@ object RealignerTargetCreator {
val
re
=
new
RealignerTargetCreator
(
root
)
re
.
input_file
:+=
input
re
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.intervals"
)
re
turn
re
re
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/SelectVariants.scala
View file @
2c323f38
...
...
@@ -18,6 +18,6 @@ object SelectVariants {
val
sv
=
new
SelectVariants
(
root
)
sv
.
variant
=
input
sv
.
out
=
output
return
sv
sv
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
2c323f38
...
...
@@ -26,8 +26,8 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
}
}
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
genotype_likelihoods_model
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypeLikelihoodsCalculationModel
.
Model
.
BOTH
nct
=
Some
(
getThreads
(
1
))
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantAnnotator.scala
View file @
2c323f38
...
...
@@ -20,6 +20,6 @@ object VariantAnnotator {
va
.
variant
=
input
va
.
input_file
=
bamFiles
va
.
out
=
output
return
va
va
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantEval.scala
View file @
2c323f38
...
...
@@ -10,8 +10,8 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
VariantEval
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantEval
with
GatkGeneral
{
override
def
beforeGraph
{
super
.
beforeGraph
override
def
beforeGraph
()
{
super
.
beforeGraph
()
}
}
...
...
@@ -22,8 +22,8 @@ object VariantEval {
vareval
.
eval
=
Seq
(
sample
)
vareval
.
comp
=
Seq
(
compareWith
)
vareval
.
out
=
output
vareval
.
beforeGraph
return
vareval
vareval
.
beforeGraph
()
vareval
}
def
apply
(
root
:
Configurable
,
sample
:
File
,
compareWith
:
File
,
...
...
@@ -36,8 +36,8 @@ object VariantEval {
vareval
.
ST
=
ST
vareval
.
noEV
=
true
vareval
.
EV
=
EV
vareval
.
beforeGraph
return
vareval
vareval
.
beforeGraph
()
vareval
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/VariantRecalibrator.scala
View file @
2c323f38
...
...
@@ -39,6 +39,6 @@ object VariantRecalibrator {
vr
.
input
:+=
input
vr
.
recal_file
=
recal_file
vr
.
tranches_file
=
tranches_file
return
vr
vr
}
}
\ No newline at end of file
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Basty.scala
View file @
2c323f38
...
...
@@ -11,6 +11,8 @@ import nl.lumc.sasc.biopet.pipelines.basty.BastyTrait
import
org.broadinstitute.gatk.queue.QScript
/**
* Basty pipeline including GATK steps
*
* Created by pjvan_thof on 3/4/15.
*/
class
Basty
(
val
root
:
Configurable
)
extends
QScript
with
BastyTrait
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkBenchmarkGenotyping.scala
View file @
2c323f38
...
...
@@ -38,7 +38,7 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
var
gvcfPool
:
List
[
File
]
=
Nil
addGenotypingPipeline
(
gvcfPool
)
while
(
todoGvcfs
.
size
>
0
)
{
while
(
todoGvcfs
.
nonEmpty
)
{
val
index
=
Random
.
nextInt
(
todoGvcfs
.
size
)
gvcfPool
::=
todoGvcfs
(
index
)
addGenotypingPipeline
(
gvcfPool
)
...
...
@@ -51,8 +51,8 @@ class GatkBenchmarkGenotyping(val root: Configurable) extends QScript with Biope
gatkGenotyping
.
inputGvcfs
=
sampleGvcf
::
gvcfPool
gatkGenotyping
.
samples
:+=
sampleName
gatkGenotyping
.
outputDir
=
new
File
(
outputDir
,
"samples_"
+
gvcfPool
.
size
)
gatkGenotyping
.
init
gatkGenotyping
.
biopetScript
gatkGenotyping
.
init
()
gatkGenotyping
.
biopetScript
()
addAll
(
gatkGenotyping
.
functions
)
}
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkGenotyping.scala
View file @
2c323f38
...
...
@@ -38,7 +38,7 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
def
biopetScript
()
{
addGenotypeGVCFs
(
inputGvcfs
,
outputFile
)
if
(
!
samples
.
is
Empty
)
{
if
(
samples
.
non
Empty
)
{
if
(
samples
.
size
>
1
)
addSelectVariants
(
outputFile
,
samples
,
new
File
(
outputDir
,
"samples/"
),
"all"
)
for
(
sample
<-
samples
)
addSelectVariants
(
outputFile
,
List
(
sample
),
new
File
(
outputDir
,
"samples/"
),
sample
)
}
...
...
@@ -47,7 +47,7 @@ class GatkGenotyping(val root: Configurable) extends QScript with BiopetQScript
def
addGenotypeGVCFs
(
gvcfFiles
:
List
[
File
],
outputFile
:
File
)
:
File
=
{
val
genotypeGVCFs
=
GenotypeGVCFs
(
this
,
gvcfFiles
,
outputFile
)
add
(
genotypeGVCFs
)
return
genotypeGVCFs
.
out
genotypeGVCFs
.
out
}
def
addSelectVariants
(
inputFile
:
File
,
samples
:
List
[
String
],
outputDir
:
File
,
name
:
String
)
{
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala
View file @
2c323f38
...
...
@@ -78,8 +78,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
val
bamFile
:
Option
[
File
]
=
if
(
config
.
contains
(
"R1"
))
{
mapping
.
input_R1
=
config
(
"R1"
)
mapping
.
input_R2
=
config
(
"R2"
)
mapping
.
init
mapping
.
biopetScript
mapping
.
init
()
mapping
.
biopetScript
()
addAll
(
mapping
.
functions
)
// Add functions of mapping to curent function pool
Some
(
mapping
.
finalBamFile
)
}
else
if
(
config
.
contains
(
"bam"
))
{
...
...
@@ -93,8 +93,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
qscript
.
add
(
samToFastq
)
mapping
.
input_R1
=
samToFastq
.
fastqR1
mapping
.
input_R2
=
Some
(
samToFastq
.
fastqR2
)
mapping
.
init
mapping
.
biopetScript
mapping
.
init
()
mapping
.
biopetScript
()
addAll
(
mapping
.
functions
)
// Add functions of mapping to curent function pool
Some
(
mapping
.
finalBamFile
)
}
else
{
...
...
@@ -106,7 +106,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if
(
readGroup
.
getLibrary
!=
libId
)
logger
.
warn
(
"Library ID readgroup in bam file is not the same"
)
if
(
readGroup
.
getSample
!=
sampleId
||
readGroup
.
getLibrary
!=
libId
)
readGroupOke
=
false
}
inputSam
.
close
inputSam
.
close
()
if
(!
readGroupOke
)
{
if
(
config
(
"correct_readgroups"
,
default
=
false
))
{
...
...
@@ -133,8 +133,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
if
(
bamFile
.
isDefined
)
{
gatkVariantcalling
.
inputBams
=
List
(
bamFile
.
get
)
gatkVariantcalling
.
variantcalling
=
config
(
"library_variantcalling"
,
default
=
false
)
gatkVariantcalling
.
init
gatkVariantcalling
.
biopetScript
gatkVariantcalling
.
init
()
gatkVariantcalling
.
biopetScript
()
addAll
(
gatkVariantcalling
.
functions
)
}
...
...
@@ -155,8 +155,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
gatkVariantcalling
.
useHaplotypecaller
=
false
gatkVariantcalling
.
useUnifiedGenotyper
=
false
}
gatkVariantcalling
.
init
gatkVariantcalling
.
biopetScript
gatkVariantcalling
.
init
()
gatkVariantcalling
.
biopetScript
()
addAll
(
gatkVariantcalling
.
functions
)
gatkVariantcalling
.
inputBams
.
foreach
(
x
=>
addAll
(
Bam2Wig
(
qscript
,
x
).
functions
))
...
...
@@ -174,7 +174,7 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
def
biopetScript
()
:
Unit
=
{
addSamplesJobs
()
addSummaryJobs
addSummaryJobs
()
}
def
addMultiSampleJobs
()
:
Unit
=
{
...
...
@@ -184,13 +184,13 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
List
(
newFile
)
}
else
externalGvcfs
++
samples
.
map
(
_
.
_2
.
gatkVariantcalling
.
scriptOutput
.
gvcfFile
)
if
(!
skipGenotyping
&&
gvcfFiles
.
size
>
0
)
{
if
(!
skipGenotyping
&&
gvcfFiles
.
nonEmpty
)
{
if
(
jointGenotyping
)
{
val
gatkGenotyping
=
new
GatkGenotyping
(
this
)
gatkGenotyping
.
inputGvcfs
=
gvcfFiles
gatkGenotyping
.
outputDir
=
new
File
(
outputDir
,
"genotyping"
)
gatkGenotyping
.
init
gatkGenotyping
.
biopetScript
gatkGenotyping
.
init
()
gatkGenotyping
.
biopetScript
()
addAll
(
gatkGenotyping
.
functions
)
var
vcfFile
=
gatkGenotyping
.
outputFile
}
...
...
@@ -216,8 +216,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
multisampleVariantcalling
.
inputBams
=
allBamfiles
.
toList
multisampleVariantcalling
.
outputDir
=
new
File
(
outputDir
,
"variantcalling"
)
multisampleVariantcalling
.
outputName
=
"multisample"
multisampleVariantcalling
.
init
multisampleVariantcalling
.
biopetScript
multisampleVariantcalling
.
init
()
multisampleVariantcalling
.
biopetScript
()
addAll
(
multisampleVariantcalling
.
functions
)
if
(
config
(
"inputtype"
,
default
=
"dna"
).
asString
!=
"rna"
&&
config
(
"recalibration"
,
default
=
false
).
asBoolean
)
{
...
...
@@ -225,8 +225,8 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
recalibration
.
inputVcf
=
multisampleVariantcalling
.
scriptOutput
.
finalVcfFile
recalibration
.
bamFiles
=
allBamfiles
recalibration
.
outputDir
=
new
File
(
outputDir
,
"recalibration"
)
recalibration
.
init
recalibration
.
biopetScript
recalibration
.
init
()
recalibration
.
biopetScript
()
}
}
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantRecalibration.scala
View file @
2c323f38
...
...
@@ -27,7 +27,7 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
}
def
biopetScript
()
{
var
vcfFile
:
File
=
if
(
!
bamFiles
.
is
Empty
)
addVariantAnnotator
(
inputVcf
,
bamFiles
,
outputDir
)
else
inputVcf
var
vcfFile
:
File
=
if
(
bamFiles
.
non
Empty
)
addVariantAnnotator
(
inputVcf
,
bamFiles
,
outputDir
)
else
inputVcf
vcfFile
=
addSnpVariantRecalibrator
(
vcfFile
,
outputDir
)
vcfFile
=
addIndelVariantRecalibrator
(
vcfFile
,
outputDir
)
}
...
...
@@ -35,41 +35,41 @@ class GatkVariantRecalibration(val root: Configurable) extends QScript with Biop
def
addSnpVariantRecalibrator
(
inputVcf
:
File
,
dir
:
File
)
:
File
=
{
val
snpRecal
=
VariantRecalibrator
(
this
,
inputVcf
,
swapExt
(
dir
,
inputVcf
,
".vcf"
,
".indel.recal"
),
swapExt
(
dir
,
inputVcf
,
".vcf"
,
".indel.tranches"
),
indel
=
false
)
if
(
!
snpRecal
.
resource
.
is
Empty
)
{
if
(
snpRecal
.
resource
.
non
Empty
)
{
add
(
snpRecal
)
val
snpApply
=
ApplyRecalibration
(
this
,
inputVcf
,
swapExt
(
dir
,
inputVcf
,
".vcf"
,
".indel.recal.vcf"
),
snpRecal
.
recal_file
,
snpRecal
.
tranches_file
,
indel
=
false
)
add
(
snpApply
)
return
snpApply
.
out
snpApply
.
out
}
else
{
logger
.
warn
(
"Skipped snp Recalibration, resource is missing"
)
return
inputVcf
inputVcf
}
}
def
addIndelVariantRecalibrator
(
inputVcf
:
File
,
dir
:
File
)
:
File
=
{
val
indelRecal
=
VariantRecalibrator
(
this
,
inputVcf
,
swapExt
(
dir
,
inputVcf
,
".vcf"
,
".indel.recal"
),
swapExt
(
dir
,
inputVcf
,
".vcf"
,
".indel.tranches"
),
indel
=
true
)
if
(
!
indelRecal
.
resource
.
is
Empty
)
{
if
(
indelRecal
.
resource
.
non
Empty
)
{
add
(
indelRecal
)
val
indelApply
=
ApplyRecalibration
(
this
,
inputVcf
,
swapExt
(
dir
,
inputVcf
,
".vcf"
,
".indel.recal.vcf"
),
indelRecal
.
recal_file
,
indelRecal
.
tranches_file
,
indel
=
true
)
add
(
indelApply
)
return
indelApply
.
out
indelApply
.
out
}
else
{
logger
.
warn
(
"Skipped indel Recalibration, resource is missing"
)
return
inputVcf
inputVcf
}
}
def
addVariantAnnotator
(
inputvcf
:
File
,
bamfiles
:
List
[
File
],
dir
:
File
)
:
File
=
{
val
variantAnnotator
=
VariantAnnotator
(
this
,
inputvcf
,
bamfiles
,
swapExt
(
dir
,
inputvcf
,
".vcf"
,
".anotated.vcf"
))
add
(
variantAnnotator
)
return
variantAnnotator
.
out
variantAnnotator
.
out
}
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
2c323f38
...
...
@@ -111,7 +111,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if
(
sampleID
!=
null
&&
(
useHaplotypecaller
||
config
(
"joint_genotyping"
,
default
=
false
).
asBoolean
))
{
val
hcGvcf
=
new
HaplotypeCaller
(
this
)
hcGvcf
.
useGvcf
hcGvcf
.
useGvcf
()
hcGvcf
.
input_file
=
scriptOutput
.
bamFiles
hcGvcf
.
out
=
new
File
(
outputDir
,
outputName
+
".hc.discovery.gvcf.vcf.gz"
)
add
(
hcGvcf
)
...
...
@@ -228,7 +228,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
indelRealigner
.
isIntermediate
=
isIntermediate
add
(
indelRealigner
)
return
indelRealigner
.
o
indelRealigner
.
o
}
def
addBaseRecalibrator
(
inputBam
:
File
,
dir
:
File
,
isIntermediate
:
Boolean
=
false
)
:
File
=
{
...
...
@@ -253,7 +253,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
printReads
.
isIntermediate
=
isIntermediate
add
(
printReads
)
return
printReads
.
o
printReads
.
o
}
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/Shiva.scala
View file @
2c323f38
...
...
@@ -12,6 +12,8 @@ import nl.lumc.sasc.biopet.pipelines.shiva.{ ShivaTrait, ShivaVariantcallingTrai
import
org.broadinstitute.gatk.queue.QScript
/**
* Shiva inplementation with GATK steps
*
* Created by pjvan_thof on 2/26/15.
*/
class
Shiva
(
val
root
:
Configurable
)
extends
QScript
with
ShivaTrait
{
...
...
@@ -47,7 +49,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
/** Return true when baserecalibration is executed */
protected
def
doneBaseRecalibrator
:
Boolean
=
{
val
br
=
new
BaseRecalibrator
(
qscript
)
useBaseRecalibration
&&
!
br
.
knownSites
.
is
Empty
useBaseRecalibration
&&
br
.
knownSites
.
non
Empty
}
/** This will adds preprocess steps, gatk indel realignment and base recalibration is included here */
...
...
@@ -70,13 +72,12 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
/** This methods will add double preprocess steps, with GATK indel realignment */
override
protected
def
addDoublePreProcess
(
input
:
List
[
File
],
isIntermediate
:
Boolean
=
false
)
:
Option
[
File
]
=
{
if
(
input
.
size
<=
1
)
super
.
addDoublePreProcess
(
input
)
else
super
.
addDoublePreProcess
(
input
,
true
).
collect
{
case
file
=>
{
else
super
.
addDoublePreProcess
(
input
,
isIntermediate
=
true
).
collect
{
case
file
=>
config
(
"use_indel_realigner"
,
default
=
true
).
asBoolean
match
{
case
true
=>
addIndelRealign
(
file
,
sampleDir
,
false
)
case
true
=>
addIndelRealign
(
file
,
sampleDir
,
isIntermediate
=
false
)
case
false
=>
file
}
}
}
}
}
...
...
@@ -91,7 +92,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
indelRealigner
.
isIntermediate
=
isIntermediate
add
(
indelRealigner
)
return
indelRealigner
.
o
indelRealigner
.
o
}
/** Adds base recalibration jobs */
...
...
@@ -117,7 +118,7 @@ class Shiva(val root: Configurable) extends QScript with ShivaTrait {
printReads
.
isIntermediate
=
isIntermediate
add
(
printReads
)
return
printReads
.
o
printReads
.
o
}
}
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcalling.scala
View file @
2c323f38
...
...
@@ -12,6 +12,8 @@ import nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
import
org.broadinstitute.gatk.queue.QScript
/**
* ShivaVariantcalling with GATK variantcallers
*
* Created by pjvan_thof on 2/26/15.
*/
class
ShivaVariantcalling
(
val
root
:
Configurable
)
extends
QScript
with
ShivaVariantcallingTrait
{
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaTest.scala
View file @
2c323f38
...
...
@@ -20,6 +20,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.
{
DataProvider
,
Test
}
/**
* Class for testing shiva
*
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaTest
extends
TestNGSuite
with
Matchers
{
...
...
@@ -48,16 +50,16 @@ class ShivaTest extends TestNGSuite with Matchers {
covariates
:
Boolean
,
realign
:
Boolean
,
baseRecalibration
:
Boolean
)
:
Unit
=
{
val
map
=
{
var
m
:
Map
[
String
,
Any
]
=
ShivaTest
.
config
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample1
,
m
.
toMap
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample2
,
m
.
toMap
)
if
(
sample3
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample3
,
m
.
toMap
)
if
(
dbsnp
)
m
=
ConfigUtils
.
mergeMaps
(
Map
(
"dbsnp"
->
"test"
),
m
.
toMap
)
if
(
sample1
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample1
,
m
)
if
(
sample2
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample2
,
m
)
if
(
sample3
)
m
=
ConfigUtils
.
mergeMaps
(
ShivaTest
.
sample3
,
m
)
if
(
dbsnp
)
m
=
ConfigUtils
.
mergeMaps
(
Map
(
"dbsnp"
->
"test"
),
m
)
ConfigUtils
.
mergeMaps
(
Map
(
"multisample_sample_variantcalling"
->
multi
,
"single_sample_variantcalling"
->
single
,
"library_variantcalling"
->
library
,
"use_analyze_covariates"
->
covariates
,
"use_indel_realigner"
->
realign
,
"use_base_recalibration"
->
baseRecalibration
),
m
.
toMap
)
"use_base_recalibration"
->
baseRecalibration
),
m
)
}
...
...
protected/biopet-gatk-pipelines/src/test/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingTest.scala
View file @
2c323f38
...
...
@@ -22,6 +22,8 @@ import org.testng.annotations.{ AfterClass, DataProvider, Test }
import
scala.collection.mutable.ListBuffer
/**
* Class for testing ShivaVariantcalling
*
* Created by pjvan_thof on 3/2/15.
*/
class
ShivaVariantcallingTest
extends
TestNGSuite
with
Matchers
{
...
...
public/bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @
2c323f38