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biopet.biopet
Commits
1c6ea1d9
Commit
1c6ea1d9
authored
Jan 20, 2015
by
Peter van 't Hof
Browse files
Fixed nullpointer
parent
33e6ef14
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
1c6ea1d9
...
...
@@ -61,7 +61,7 @@ trait MultiSampleQScript extends BiopetQScript {
for
(
sampleID
<-
getSamples
)
{
currentSample
=
Some
(
sampleID
)
samplesOutput
+=
sampleID
->
runSingleSampleJobs
(
sampleID
)
currentSample
=
null
currentSample
=
None
}
}
...
...
@@ -136,9 +136,15 @@ trait MultiSampleQScript extends BiopetQScript {
}
override
protected
[
core
]
def
configFullPath
:
List
[
String
]
=
{
(
if
(
currentSample
.
isDefined
)
"samples"
::
currentSample
.
get
::
Nil
else
Nil
)
:::
(
if
(
currentLibrary
.
isDefined
)
"libraries"
::
currentLibrary
.
get
::
Nil
else
Nil
)
:::
super
.
configFullPath
val
s
=
currentSample
match
{
case
Some
(
s
)
=>
"samples"
::
s
::
Nil
case
_
=>
Nil
}
val
l
=
currentLibrary
match
{
case
Some
(
l
)
=>
"libraries"
::
l
::
Nil
case
_
=>
Nil
}
s
:::
l
:::
super
.
configFullPath
}
override
val
config
=
new
ConfigFunctionsExt
...
...
@@ -151,8 +157,8 @@ trait MultiSampleQScript extends BiopetQScript {
freeVar
:
Boolean
=
true
,
sample
:
String
=
null
,
library
:
String
=
null
)
:
ConfigValue
=
{
val
s
=
if
(
sample
==
null
)
currentSample
.
getOrElse
(
null
)
else
sample
val
l
=
if
(
library
==
null
)
currentLibrary
.
getOrElse
(
null
)
else
library
val
s
=
currentSample
.
getOrElse
(
sample
)
val
l
=
currentLibrary
.
getOrElse
(
library
)
super
.
apply
(
key
,
default
,
submodule
,
required
,
freeVar
,
s
,
l
)
}
...
...
@@ -161,8 +167,8 @@ trait MultiSampleQScript extends BiopetQScript {
freeVar
:
Boolean
=
true
,
sample
:
String
=
null
,
library
:
String
=
null
)
=
{
val
s
=
if
(
sample
==
null
)
currentSample
.
getOrElse
(
null
)
else
sample
val
l
=
if
(
library
==
null
)
currentLibrary
.
getOrElse
(
null
)
else
library
val
s
=
currentSample
.
getOrElse
(
sample
)
val
l
=
currentLibrary
.
getOrElse
(
library
)
super
.
contains
(
key
,
submodule
,
freeVar
,
s
,
l
)
}
}
...
...
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