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biopet.biopet
Commits
53da62be
Commit
53da62be
authored
Nov 24, 2016
by
Sander Bollen
Browse files
fix some more
parent
3ce114fa
Changes
2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
View file @
53da62be
...
...
@@ -11,6 +11,6 @@ abstract class Xhmm extends BiopetCommandLineFunction with Version {
executable
=
config
(
"exe"
,
namespace
=
"xhmm"
,
default
=
"xhmm"
)
def
versionCommand
=
executable
+
required
(
"--version"
)
def
versionCommand
=
executable
+
"
--version"
def
versionRegex
=
"""xhmm (.*)"""
.
r
}
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
53da62be
...
...
@@ -94,6 +94,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
val
genotype
=
new
XhmmGenotype
(
this
)
genotype
.
inputXcnv
=
discover
.
outputXcnv
genotype
.
inputMatrix
=
secondMatrix
.
outputMatrix
genotype
.
r
=
thirdMatrix
.
outputMatrix
genotype
.
outputVcf
=
new
File
(
xhmmDir
,
"xhmm.vcf"
)
add
(
genotype
)
...
...
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