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biopet.biopet
Commits
cfdfd0b9
Commit
cfdfd0b9
authored
Oct 08, 2015
by
Sander van der Zeeuw
Browse files
added bam metrics for filtered file
parent
e93bf522
Changes
1
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public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
cfdfd0b9
...
...
@@ -124,11 +124,20 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
val
bamMetrics
=
BamMetrics
(
qscript
,
bamFile
,
new
File
(
sampleDir
,
"metrics"
),
sampleId
=
Some
(
sampleId
))
addAll
(
bamMetrics
.
functions
)
addSummaryQScript
(
bamMetrics
)
val
bamMetricsFilter
=
BamMetrics
(
qscript
,
bamFileFilter
,
new
File
(
sampleDir
,
"metrics-filter"
),
sampleId
=
Some
(
sampleId
))
addAll
(
bamMetricsFilter
.
functions
)
bamMetricsFilter
.
summaryName
=
"bamMetrics-filter"
addSummaryQScript
(
bamMetricsFilter
)
addAll
(
Bam2Wig
(
qscript
,
bamFile
).
functions
)
addAll
(
Bam2Wig
(
qscript
,
bamFileFilter
).
functions
)
val
samtoolsView
=
new
SamtoolsView
(
qscript
)
samtoolsView
.
input
=
bamFile
samtoolsView
.
output
=
bamFileFilter
samtoolsView
.
b
=
true
samtoolsView
.
h
=
true
add
(
samtoolsView
)
val
buildBamIndex
=
new
BuildBamIndex
(
qscript
)
...
...
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