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biopet.biopet
Commits
ebe731f3
Commit
ebe731f3
authored
Feb 03, 2015
by
Peter van 't Hof
Browse files
Fix for -sample commandline argument
parent
d46ad182
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MultiSampleQScript.scala
View file @
ebe731f3
...
...
@@ -125,15 +125,15 @@ trait MultiSampleQScript extends BiopetQScript {
val
samples
:
Map
[
String
,
Sample
]
=
sampleIds
.
map
(
id
=>
id
->
makeSample
(
id
)).
toMap
/** Returns a list of all sampleIDs */
protected
def
sampleIds
:
Set
[
String
]
=
if
(
onlySample
!=
Nil
)
onlySample
.
toSet
else
{
ConfigUtils
.
any2map
(
Config
.
global
.
map
(
"samples"
)).
keySet
}
protected
def
sampleIds
:
Set
[
String
]
=
ConfigUtils
.
any2map
(
Config
.
global
.
map
(
"samples"
)).
keySet
/** Runs addAndTrackJobs method for each sample */
final
def
addSamplesJobs
()
{
for
((
sampleId
,
sample
)
<-
samples
)
{
sample
.
addAndTrackJobs
()
}
if
(
onlySample
.
isEmpty
)
samples
.
foreach
{
case
(
sampleId
,
sample
)
=>
sample
.
addAndTrackJobs
()
}
else
onlySample
.
foreach
(
sampleId
=>
samples
.
get
(
sampleId
)
match
{
case
Some
(
sample
)
=>
sample
.
addAndTrackJobs
()
case
None
=>
logger
.
warn
(
"sampleId '"
+
sampleId
+
"' not found"
)
})
}
/** Stores sample state */
...
...
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