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biopet.biopet
Commits
55378379
Commit
55378379
authored
Jan 21, 2015
by
Peter van 't Hof
Browse files
Change sample to var
parent
36c29d93
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
55378379
...
...
@@ -31,8 +31,10 @@ trait MultiSampleQScript extends BiopetQScript {
type
Sample
<:
AbstractSample
abstract
class
AbstractSample
{
val
sampleId
:
String
val
config
=
new
ConfigFunctions
(
defaultSample
=
Some
(
sampleId
))
abstract
class
AbstractLibrary
{
val
libraryId
:
String
val
config
=
new
ConfigFunctions
(
defaultSample
=
Some
(
sampleId
),
defaultLibrary
=
Some
(
libraryId
))
final
def
run
()
:
Unit
=
{
currentSample
=
Some
(
sampleId
)
currentLibrary
=
Some
(
libraryId
)
...
...
@@ -74,7 +76,7 @@ trait MultiSampleQScript extends BiopetQScript {
}
}
va
l
samples
:
Map
[
String
,
Sample
]
va
r
samples
:
Map
[
String
,
Sample
]
=
Map
()
/** Returns a list of all sampleIDs */
protected
def
getSamplesIds
:
Set
[
String
]
=
if
(
onlySample
!=
Nil
)
onlySample
.
toSet
else
{
...
...
@@ -102,30 +104,4 @@ trait MultiSampleQScript extends BiopetQScript {
}
s
:::
l
:::
super
.
configFullPath
}
override
val
config
=
new
ConfigFunctionsExt
protected
class
ConfigFunctionsExt
extends
super
.
ConfigFunctions
{
override
def
apply
(
key
:
String
,
default
:
Any
=
null
,
submodule
:
String
=
null
,
required
:
Boolean
=
false
,
freeVar
:
Boolean
=
true
,
sample
:
String
=
null
,
library
:
String
=
null
)
:
ConfigValue
=
{
val
s
=
currentSample
.
getOrElse
(
sample
)
val
l
=
currentLibrary
.
getOrElse
(
library
)
super
.
apply
(
key
,
default
,
submodule
,
required
,
freeVar
,
s
,
l
)
}
override
def
contains
(
key
:
String
,
submodule
:
String
=
null
,
freeVar
:
Boolean
=
true
,
sample
:
String
=
null
,
library
:
String
=
null
)
=
{
val
s
=
currentSample
.
getOrElse
(
sample
)
val
l
=
currentLibrary
.
getOrElse
(
library
)
super
.
contains
(
key
,
submodule
,
freeVar
,
s
,
l
)
}
}
}
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