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biopet.biopet
Commits
03af79a2
Commit
03af79a2
authored
Nov 23, 2016
by
Sander Bollen
Browse files
mergegatkdepths wrapper
parent
c79918d9
Changes
1
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
0 → 100644
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03af79a2
package
nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmMergeGatkDepths
(
val
root
:
Configurable
)
extends
Xhmm
{
@Input
(
doc
=
"List of input depths files"
)
var
gatkDepthsFiles
:
List
[
File
]
=
Nil
@Output
(
doc
=
"Merged output file in XHMM format"
)
var
output
:
File
=
_
def
cmdLine
=
{
executable
+
repeat
(
"--GATKdepths"
,
gatkDepthsFiles
)
+
required
(
"-o"
,
output
)
}
}
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