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biopet.biopet
Commits
77d06f6e
Commit
77d06f6e
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Fix output bam files of mapping
parent
73995acb
Changes
1
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
77d06f6e
...
...
@@ -51,6 +51,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
mapping
.
sampleId
=
Some
(
sampleId
)
mapping
.
libId
=
Some
(
libId
)
mapping
.
outputDir
=
libDir
mapping
.
outputName
=
sampleId
+
"-"
+
libId
(
Some
(
mapping
),
Some
(
mapping
.
finalBamFile
),
preProcess
(
mapping
.
finalBamFile
))
}
...
...
@@ -187,7 +188,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
val
bamMetrics
=
new
BamMetrics
(
root
)
bamMetrics
.
sampleId
=
Some
(
sampleId
)
bamMetrics
.
inputBam
=
preProcessBam
.
get
bamMetrics
.
outputDir
=
output
Dir
bamMetrics
.
outputDir
=
sample
Dir
bamMetrics
.
init
bamMetrics
.
biopetScript
addAll
(
bamMetrics
.
functions
)
...
...
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