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biopet.biopet
Commits
ba3725c3
Commit
ba3725c3
authored
Jul 18, 2017
by
pjvan_thof
Browse files
Fix compile errors
parent
3835e14b
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverFixVCF.scala
View file @
ba3725c3
...
...
@@ -20,7 +20,7 @@ package nl.lumc.sasc.biopet.extensions.clever
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.utils.ToolCommand
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
...
...
@@ -48,9 +48,8 @@ class CleverFixVCF(val parent: Configurable) extends BiopetJavaCommandLineFuncti
object
CleverFixVCF
extends
ToolCommand
{
case
class
Args
(
inputVCF
:
File
=
null
,
sampleLabel
:
String
=
""
,
outputVCF
:
File
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'i'
,
"inputvcf"
)
required
()
valueName
"<vcffile/path>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputVCF
=
x
)
}
text
"Please specify the input Clever VCF file"
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/pindel/PindelConfig.scala
View file @
ba3725c3
...
...
@@ -18,7 +18,7 @@ import java.io.{File, PrintWriter}
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
ToolCommand
}
import
nl.lumc.sasc.biopet.utils.
{
AbstractOptParser
,
BamUtils
,
ToolCommand
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
class
PindelConfig
(
val
parent
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
...
...
@@ -46,9 +46,8 @@ object PindelConfig extends ToolCommand {
sampleLabel
:
Option
[
String
]
=
None
,
insertSize
:
Option
[
Int
]
=
None
,
output
:
Option
[
File
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
class
OptParser
extends
AbstractOptParser
[
Args
](
commandName
)
{
opt
[
File
](
'i'
,
"inputbam"
)
required
()
valueName
"<bamfile/path>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputBam
=
x
)
}
text
"Please specify the input bam file"
...
...
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