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biopet.biopet
Commits
a2f2c807
Commit
a2f2c807
authored
Nov 28, 2016
by
Sander Bollen
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fix more arguments
parent
c91a9617
Changes
2
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2 changed files
with
5 additions
and
1 deletion
+5
-1
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
...la/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
+1
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
...cala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
+4
-1
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
View file @
a2f2c807
...
...
@@ -38,6 +38,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
required
(
"-R"
,
r
)
+
required
(
"-c"
,
outputXcnv
)
+
required
(
"-a"
,
outputXcnvAuxFile
)
+
required
(
"-p"
,
discoverParamsFile
)
+
required
(
"-s"
,
xhmmAnalysisName
)
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
View file @
a2f2c807
...
...
@@ -65,7 +65,10 @@ class XhmmMatrix(val root: Configurable) extends Xhmm {
if
(
inputExcludeSamples
.
nonEmpty
&&
inputExcludeTargets
.
nonEmpty
)
{
repeat
(
"--excludeTargets"
,
inputExcludeTargets
)
+
repeat
(
"--excludeSamples"
,
inputExcludeSamples
)
}
else
if
(
centerData
&&
zScoreData
)
{
conditional
(
centerData
,
"--centerData"
)
+
conditional
(
zScoreData
,
"--centerData"
)
+
required
(
"--maxSdTargetRD"
,
maxsdTargetRD
)
conditional
(
centerData
,
"--centerData"
)
+
required
(
"--centerType"
,
centerType
)
+
conditional
(
zScoreData
,
"--zScoreData"
)
+
required
(
"--maxSdTargetRD"
,
maxsdTargetRD
)
}
else
{
required
(
"--minTargetSize"
,
minTargetSize
)
+
required
(
"--maxTargetSize"
,
maxTargetSize
)
+
...
...
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