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biopet.biopet
Commits
76992696
Commit
76992696
authored
May 06, 2016
by
Peter van 't Hof
Browse files
Update catvariants
parent
556ca42a
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CatVariants.scala
View file @
76992696
...
...
@@ -2,11 +2,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
nl.lumc.sasc.biopet.core.
{
BiopetJavaCommandLineFunction
,
Reference
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Gather
,
Input
,
Output
}
class
CatVariants
(
val
root
:
Configurable
)
extends
BiopetJavaCommandLineFunction
{
class
CatVariants
(
val
root
:
Configurable
)
extends
BiopetJavaCommandLineFunction
with
Reference
{
analysisName
=
"CatVariants"
javaMainClass
=
"org.broadinstitute.gatk.tools.CatVariants"
...
...
@@ -44,6 +44,11 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
@Gather
(
classOf
[
org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction
])
var
log_to_file
:
File
=
_
override
def
beforeGraph
()
=
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-R"
,
reference
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-V"
,
variant
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
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