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biopet.biopet
Commits
9b20e271
Commit
9b20e271
authored
Aug 22, 2014
by
Peter van 't Hof
Browse files
Added skipMetrics option
parent
f6bbd1b0
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
9b20e271
...
...
@@ -33,6 +33,9 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
@Argument
(
doc
=
"Skip mark duplicates"
,
shortName
=
"skipmarkduplicates"
,
required
=
false
)
var
skipMarkduplicates
:
Boolean
=
false
@Argument
(
doc
=
"Skip metrics"
,
shortName
=
"skipmetrics"
,
required
=
false
)
var
skipMetrics
:
Boolean
=
false
@Argument
(
doc
=
"Alginer"
,
shortName
=
"ALN"
,
required
=
false
)
var
aligner
:
String
=
_
...
...
@@ -217,7 +220,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
add
(
MarkDuplicates
(
this
,
bamFiles
,
bamFile
))
}
else
if
(
skipMarkduplicates
&&
chunking
)
bamFile
=
addMergeBam
(
bamFiles
,
new
File
(
outputDir
+
outputName
+
".bam"
),
outputDir
)
addAll
(
BamMetrics
.
apply
(
this
,
bamFile
,
outputDir
+
"metrics/"
).
functions
)
if
(!
skipMetrics
)
addAll
(
BamMetrics
.
apply
(
this
,
bamFile
,
outputDir
+
"metrics/"
).
functions
)
outputFiles
+=
(
"finalBamFile"
->
bamFile
)
}
...
...
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