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biopet.biopet
Commits
5760560d
Commit
5760560d
authored
Jul 10, 2017
by
Peter van 't Hof
Browse files
Fixing compile issues
parent
e8609425
Changes
2
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/MuTect2.scala
View file @
5760560d
...
...
@@ -3,9 +3,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.ScatterGatherableFunction
import
nl.lumc.sasc.biopet.extensions.gatk.CommandLineGATK.isFileWithTag
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
Output
}
class
MuTect2
(
val
parent
:
Configurable
)
extends
CommandLineGATK
with
ScatterGatherableFunction
{
...
...
@@ -181,8 +179,7 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
@Argument
(
fullName
=
"useNewAFCalculator"
,
shortName
=
"newQual"
,
required
=
false
)
var
useNewAFCalculator
:
Boolean
=
config
(
"use_new_af_calculator"
,
default
=
false
)
override
def
cmdLine
=
super
.
cmdLine
+
override
def
cmdLine
:
String
=
super
.
cmdLine
+
optional
(
"--cosmic"
,
cosmic
)
+
optional
(
"--dbsnp"
,
dbsnp
)
+
optional
(
"--normal_panel"
,
ponFile
)
+
...
...
@@ -213,13 +210,3 @@ class MuTect2(val parent: Configurable) extends CommandLineGATK with ScatterGath
conditional
(
useNewAFCalculator
,
"--useNewAFCalculator"
)
+
(
if
(
outputAsStdout
)
""
else
required
(
"--out"
,
outputVcf
))
}
object
MuTect2
{
def
apply
(
parent
:
Configurable
,
tumorSampleBam
:
File
,
normalSampleBam
:
File
,
output
:
File
)
:
MuTect2
=
{
val
mutect2
=
new
MuTect2
(
parent
)
mutect2
.
tumorSampleBam
=
tumorSampleBam
mutect2
.
normalSampleBam
=
normalSampleBam
mutect2
.
outputVcf
=
output
mutect2
}
}
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
View file @
5760560d
...
...
@@ -416,8 +416,8 @@ object ConfigUtils extends Logging {
Logging
.
addError
(
"Value does not exist but is required, key: "
+
value
.
requestIndex
.
key
+
" namespace: "
+
value
.
requestIndex
.
module
,
if
(
value
.
requestIndex
.
path
!=
Nil
)
" path: "
+
value
.
requestIndex
.
path
.
mkString
(
"->"
)
else
null
if
(
value
.
requestIndex
.
path
!=
Nil
)
Some
(
" path: "
+
value
.
requestIndex
.
path
.
mkString
(
"->"
)
)
else
None
)
exist
}
...
...
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