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biopet.biopet
Commits
2ca6260e
Commit
2ca6260e
authored
Jul 21, 2017
by
pjvan_thof
Browse files
Fixing duplicate metrics
parent
67f8439a
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
2ca6260e
...
...
@@ -231,14 +231,15 @@ trait MultisampleMappingTrait extends MultiSampleQScript with Reference { qscrip
}
else
add
(
Ln
.
linkBamFile
(
qscript
,
inputBam
.
get
,
bamFile
.
get
)
:
_
*
)
}
val
bamMetrics
=
new
BamMetrics
(
qscript
)
bamMetrics
.
sampleId
=
Some
(
sampleId
)
bamMetrics
.
libId
=
Some
(
libId
)
bamMetrics
.
inputBam
=
bamFile
.
get
bamMetrics
.
outputDir
=
new
File
(
libDir
,
"metrics"
)
bamMetrics
.
paired
=
inputR2
.
isDefined
||
inputBam
.
isDefined
add
(
bamMetrics
)
if
(!
bamToFastq
)
{
val
bamMetrics
=
new
BamMetrics
(
qscript
)
bamMetrics
.
sampleId
=
Some
(
sampleId
)
bamMetrics
.
libId
=
Some
(
libId
)
bamMetrics
.
inputBam
=
bamFile
.
get
bamMetrics
.
outputDir
=
new
File
(
libDir
,
"metrics"
)
bamMetrics
.
paired
=
inputR2
.
isDefined
||
inputBam
.
isDefined
add
(
bamMetrics
)
}
if
(
config
(
"execute_bam2wig"
,
default
=
true
))
add
(
Bam2Wig
(
qscript
,
bamFile
.
get
))
}
else
logger
.
warn
(
s
"Sample '$sampleId' does not have any input files"
)
...
...
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