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biopet.biopet
Commits
1c1ac1f0
Commit
1c1ac1f0
authored
Feb 16, 2015
by
Peter van 't Hof
Browse files
Remove unused apply methods
parent
e42e39c6
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/samtools/SamtoolsFlagstat.scala
View file @
1c1ac1f0
...
...
@@ -36,16 +36,4 @@ object SamtoolsFlagstat {
flagstat
.
output
=
output
return
flagstat
}
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
SamtoolsFlagstat
=
{
val
dir
=
if
(
outputDir
.
endsWith
(
"/"
))
outputDir
else
outputDir
+
"/"
val
outputFile
=
new
File
(
dir
+
swapExtension
(
input
.
getName
))
return
apply
(
root
,
input
,
outputFile
)
}
def
apply
(
root
:
Configurable
,
input
:
File
)
:
SamtoolsFlagstat
=
{
return
apply
(
root
,
input
,
new
File
(
swapExtension
(
input
.
getAbsolutePath
)))
}
private
def
swapExtension
(
inputFile
:
String
)
=
inputFile
.
stripSuffix
(
".bam"
)
+
".flagstat"
}
\ No newline at end of file
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