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biopet.biopet
Commits
997c7f15
Commit
997c7f15
authored
Nov 23, 2016
by
Sander Bollen
Browse files
xhmm genotype wrapper
parent
3f5dd689
Changes
1
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
0 → 100644
View file @
997c7f15
package
nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmGenotype
(
val
root
:
Configurable
)
extends
Xhmm
with
Reference
{
@Input
var
inputMatrix
:
File
=
_
@Input
var
inputXcnv
:
File
=
_
@Output
var
outputVcf
:
File
=
_
@Input
var
r
:
File
=
_
@Argument
var
discoverParamsFile
:
File
=
config
(
"discover_params"
,
namespace
=
"xhmm"
)
def
cmdLine
=
{
executable
+
required
(
"--genotype"
)
+
required
(
"-p"
,
discoverParamsFile
)
+
required
(
"-r"
,
inputMatrix
)
+
required
(
"-R"
,
r
)
+
required
(
"-g"
,
inputXcnv
)
+
required
(
"-F"
,
referenceFasta
())
+
required
(
"-v"
,
outputVcf
)
}
}
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