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biopet.biopet
Commits
a2910fa6
Commit
a2910fa6
authored
Jun 12, 2017
by
pjvan_thof
Browse files
Fixing code warnings
parent
5f23d851
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/MarkDuplicates.scala
View file @
a2910fa6
...
...
@@ -78,7 +78,7 @@ class MarkDuplicates(val parent: Configurable) extends Picard with Summarizable
}
/** Returns command to execute */
override
def
cmdLine
=
override
def
cmdLine
:
String
=
super
.
cmdLine
+
repeat
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
+
...
...
@@ -108,7 +108,7 @@ class MarkDuplicates(val parent: Configurable) extends Picard with Summarizable
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
=
Picard
.
getMetrics
(
outputMetrics
).
getOrElse
(
Map
())
def
summaryStats
:
Any
=
Picard
.
getMetrics
(
outputMetrics
).
getOrElse
(
Map
())
}
object
MarkDuplicates
{
...
...
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