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biopet.biopet
Commits
cf338a86
Commit
cf338a86
authored
Nov 23, 2015
by
Peter van 't Hof
Browse files
Adding vt decompose extension
parent
ac9315e7
Changes
1
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/vt/VtDecompose.scala
0 → 100644
View file @
cf338a86
package
nl.lumc.sasc.biopet.extensions.vt
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
Version
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by pjvanthof on 20/11/15.
*/
class
VtDecompose
(
val
root
:
Configurable
)
extends
Vt
with
Version
with
Reference
{
def
versionRegex
=
"""decompose (.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
def
versionCommand
=
executable
+
" decompose"
@Input
(
required
=
true
)
var
inputVcf
:
File
=
_
@Output
(
required
=
true
)
var
outputVcf
:
File
=
_
var
intervalsFile
:
Option
[
File
]
=
config
(
"intervals_file"
)
val
smartDecompose
:
Boolean
=
config
(
"smart_decompose"
,
default
=
false
)
def
cmdLine
=
required
(
executable
)
+
required
(
"decompose"
)
+
required
(
"-o"
,
outputVcf
)
+
optional
(
"-I"
,
intervalsFile
)
+
conditional
(
smartDecompose
,
"-s"
)
+
required
(
inputVcf
)
}
\ No newline at end of file
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