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biopet.biopet
Commits
b32296d9
Commit
b32296d9
authored
Mar 22, 2017
by
Peter van 't Hof
Browse files
Checking content of insertsize metrics
parent
50b8f109
Changes
1
Show whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
b32296d9
...
@@ -59,7 +59,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
...
@@ -59,7 +59,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
library
=
NoLibrary
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
library
=
NoLibrary
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
val
rnaExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"bammetrics"
,
"rna"
,
val
rnaExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"bammetrics"
,
"rna"
,
library
=
NoLibrary
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
library
=
NoLibrary
,
mustHaveSample
=
true
),
Duration
.
Inf
)
>=
1
val
insertsizeExecuted
=
summary
.
getS
etting
sForSamples
(
runId
,
pipelineName
,
NoModule
,
keyValues
=
Map
()).
count
(
_
.
_2
(
"paired"
)
==
So
me
(
tr
ue
))
>=
1
val
insertsizeExecuted
=
summary
.
getS
tat
sForSamples
(
runId
,
"bammetrics"
,
"CollectInsertSizeMetrics"
,
keyValues
=
Map
(
"metrics"
->
List
(
"metrics"
))).
exists
(
_
.
_2
(
"
metr
ics"
).
isDefined
)
val
mappingExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"mapping"
,
NoModule
,
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
val
mappingExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"mapping"
,
NoModule
,
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
val
mappingSettings
=
summary
.
getSettingsForLibraries
(
runId
,
"mapping"
,
NoModule
,
keyValues
=
Map
(
"paired"
->
List
(
"paired"
)))
val
mappingSettings
=
summary
.
getSettingsForLibraries
(
runId
,
"mapping"
,
NoModule
,
keyValues
=
Map
(
"paired"
->
List
(
"paired"
)))
val
pairedFound
=
!
mappingExecuted
||
mappingSettings
.
exists
(
_
.
_2
.
exists
(
_
.
_2
==
Option
(
true
)))
val
pairedFound
=
!
mappingExecuted
||
mappingSettings
.
exists
(
_
.
_2
.
exists
(
_
.
_2
==
Option
(
true
)))
...
...
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