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biopet.biopet
Commits
a35c3c9c
Commit
a35c3c9c
authored
Jan 18, 2016
by
Sander van der Zeeuw
Browse files
remove function removeEmptyPile()
parent
7a5e1b5c
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
View file @
a35c3c9c
...
...
@@ -39,7 +39,7 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
val
sampleFile
=
new
File
(
outputDir
,
s
"$sample.name.txt"
)
sampleFile
.
getParentFile
.
mkdirs
()
sampleFile
.
deleteOnExit
()
//
sampleFile.deleteOnExit()
val
writer
=
new
PrintWriter
(
sampleFile
)
writer
.
println
(
sample
)
writer
.
close
()
...
...
@@ -51,17 +51,10 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
def
cmdLine
=
getPythonCommand
}
def
removeEmptyPile
()
=
new
BiopetCommandLineFunction
{
override
val
root
:
Configurable
=
this
.
root
override
def
configName
=
"remove_empty_pile"
executable
=
config
(
"exe"
,
default
=
"grep"
,
freeVar
=
false
)
override
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"-vP"
)
+
required
(
"""\t\t"""
)
}
val
varscan
=
new
VarscanMpileup2cns
(
this
)
varscan
.
vcfSampleList
=
Some
(
sampleVcf
)
add
(
mpileup
|
fixMpileup
|
removeEmptyPile
()
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
)
add
(
mpileup
|
fixMpileup
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
)
add
(
Tabix
(
this
,
sampleVcf
))
sampleVcf
...
...
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