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biopet.biopet
Commits
328be9a6
Commit
328be9a6
authored
Jan 18, 2016
by
Sander van der Zeeuw
Browse files
added fixmpileup script and removeEmptypile function
parent
43748908
Changes
1
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Inline
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/VarscanCnsSingleSample.scala
View file @
328be9a6
...
...
@@ -2,6 +2,8 @@ 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
...
...
@@ -20,12 +22,12 @@ class VarscanCnsSingleSample(val root: Configurable) extends Variantcaller {
"disable_baq"
->
true
,
"depth"
->
1000000
),
"mpileup2cns"
->
Map
(
"strand_filter"
->
0
)
"
varscan
mpileup2cns"
->
Map
(
"strand_filter"
->
0
)
)
override
def
fixedValues
=
Map
(
"samtoolsmpileup"
->
Map
(
"output_mapping_quality"
->
true
),
"mpileup2cns"
->
Map
(
"output_vcf"
->
1
)
"
varscan
mpileup2cns"
->
Map
(
"output_vcf"
->
1
)
)
def
biopetScript
:
Unit
=
{
...
...
@@ -42,10 +44,24 @@ 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
}
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
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
)
add
(
mpileup
|
fixMpileup
|
removeEmptyPile
()
|
varscan
|
new
Bgzip
(
this
)
>
sampleVcf
)
add
(
Tabix
(
this
,
sampleVcf
))
sampleVcf
...
...
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