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biopet.biopet
Commits
ca40d875
Commit
ca40d875
authored
Jan 19, 2016
by
Sander van der Zeeuw
Browse files
move varscan wrapper to extensions
parent
bb46c239
Changes
3
Hide whitespace changes
Inline
Side-by-side
public/
shiva
/src/main/resources/nl/lumc/sasc/biopet/
pipelines/shi
va
/
sc
ripts
/fix_mpileup.py
→
public/
biopet-extensions
/src/main/resources/nl/lumc/sasc/biopet/
extensions/
va
r
sc
an
/fix_mpileup.py
View file @
ca40d875
File moved
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/FixMpileup.scala
0 → 100644
View file @
ca40d875
package
nl.lumc.sasc.biopet.extensions.varscan
import
nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by sajvanderzeeuw on 19-1-16.
*/
class
FixMpileup
(
val
root
:
Configurable
)
extends
PythonCommandLineFunction
{
setPythonScript
(
"fix_mpileup.py"
,
"/nl/lumc/sasc/biopet/extensions/varscan/"
)
def
cmdLine
=
getPythonCommand
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
View file @
ca40d875
...
...
@@ -2,12 +2,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.extensions.PythonCommandLineFunction
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.
{
Ln
,
Tabix
,
Bgzip
}
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.extensions.varscan.VarscanMpileup2cns
import
nl.lumc.sasc.biopet.extensions.varscan.
{
FixMpileup
,
VarscanMpileup2cns
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Tabix
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
...
...
@@ -44,17 +42,10 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
writer
.
println
(
sample
)
writer
.
close
()
val
fixMpileup
=
new
PythonCommandLineFunction
{
setPythonScript
(
"fix_mpileup.py"
,
"/nl/lumc/sasc/biopet/pipelines/shiva/scripts/"
)
override
val
root
:
Configurable
=
this
.
root
override
def
configName
=
"fix_mpileup"
def
cmdLine
=
getPythonCommand
}
val
varscan
=
new
VarscanMpileup2cns
(
this
)
varscan
.
vcfSampleList
=
Some
(
sampleFile
)
add
(
mpileup
|
f
ixMpileup
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
)
add
(
mpileup
|
new
F
ixMpileup
(
this
)
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
)
add
(
Tabix
(
this
,
sampleVcf
))
sampleVcf
...
...
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