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biopet.biopet
Commits
a13b0d1d
Commit
a13b0d1d
authored
Jan 19, 2016
by
Peter van 't Hof
Browse files
Added version to varscan
parent
3fb6b5f8
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Mpileup2cns.scala
View file @
a13b0d1d
...
...
@@ -39,6 +39,8 @@ class Mpileup2cns(val root: Configurable) extends Varscan {
var
vcfSampleList
:
Option
[
File
]
=
config
(
"vcf_sample_list"
)
var
variants
:
Option
[
Int
]
=
config
(
"variants"
)
override
def
defaultCoreMemory
=
6.0
override
def
beforeGraph
()
:
Unit
=
{
val
validValues
:
Set
[
Int
]
=
Set
(
0
,
1
)
// check for boolean vars that are passed as ints
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/varscan/Varscan.scala
View file @
a13b0d1d
...
...
@@ -15,20 +15,15 @@
*/
package
nl.lumc.sasc.biopet.extensions.varscan
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetJavaCommandLineFunction
}
abstract
class
Varscan
extends
BiopetJavaCommandLineFunction
{
abstract
class
Varscan
extends
BiopetJavaCommandLineFunction
with
Version
{
override
def
subPath
=
"varscan"
::
super
.
subPath
jarFile
=
config
(
"varscan_jar"
)
/**
* TODO: test version
* override def versionCommand = super.commandLine
* override val versionRegex = """VarScan v(.*)""".r
*/
override
def
defaultCoreMemory
=
5.0
def
versionCommand
=
super
.
commandLine
def
versionRegex
=
"""VarScan v(.*)"""
.
r
}
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