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biopet.biopet
Commits
f4ab0677
Commit
f4ab0677
authored
Jan 14, 2017
by
Peter van 't Hof
Browse files
Fix BIOPET-379
parent
2cf328c5
Changes
1
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
f4ab0677
...
...
@@ -141,9 +141,15 @@ trait MultiSampleQScript extends SummaryQScript { qscript: QScript =>
/** returns a set with library names or throws error when not found */
protected
def
libIds
:
Set
[
String
]
=
{
val
ids
=
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
val
ids
:
Set
[
String
]
=
try
{
ConfigUtils
.
getMapFromPath
(
globalConfig
.
map
,
List
(
"samples"
,
sampleId
,
"libraries"
)).
getOrElse
(
Map
()).
keySet
}
catch
{
case
e
:
IllegalStateException
if
e.getMessage
=
=
"Value is not a map: library"
=>
Logging
.
addError
(
"libraries is not a map"
)
Set
(
"placeholder"
)
}
if
(
ids
.
isEmpty
)
{
throw
new
IllegalStateException
(
s
"No libraries found in config for sample $sampleId"
)
Logging
.
addError
(
s
"No libraries found in config for sample $sampleId"
)
}
ids
}
...
...
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