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biopet.biopet
Commits
14fe91d9
Commit
14fe91d9
authored
Jan 16, 2015
by
Peter van 't Hof
Browse files
Remove unused function
parent
6c8f5376
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
14fe91d9
...
...
@@ -307,25 +307,5 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
}
object
Mapping
extends
PipelineCommand
{
def
loadFromLibraryConfig
(
root
:
Configurable
,
runConfig
:
Map
[
String
,
Any
],
sampleConfig
:
Map
[
String
,
Any
],
runDir
:
String
,
startJobs
:
Boolean
=
true
)
:
Mapping
=
{
val
mapping
=
new
Mapping
(
root
)
logger
.
debug
(
"Mapping runconfig: "
+
runConfig
)
if
(
runConfig
.
contains
(
"R1"
))
mapping
.
input_R1
=
new
File
(
runConfig
(
"R1"
).
toString
)
if
(
runConfig
.
contains
(
"R2"
))
mapping
.
input_R2
=
new
File
(
runConfig
(
"R2"
).
toString
)
mapping
.
paired
=
(
mapping
.
input_R2
!=
null
)
mapping
.
RGLB
=
runConfig
(
"ID"
).
toString
mapping
.
RGSM
=
sampleConfig
(
"ID"
).
toString
if
(
runConfig
.
contains
(
"PL"
))
mapping
.
RGPL
=
runConfig
(
"PL"
).
toString
if
(
runConfig
.
contains
(
"PU"
))
mapping
.
RGPU
=
runConfig
(
"PU"
).
toString
if
(
runConfig
.
contains
(
"CN"
))
mapping
.
RGCN
=
runConfig
(
"CN"
).
toString
mapping
.
outputDir
=
runDir
if
(
startJobs
)
{
mapping
.
init
mapping
.
biopetScript
}
return
mapping
}
}
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