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biopet.biopet
Commits
cf99b25d
Commit
cf99b25d
authored
May 31, 2016
by
Wai Yi Leung
Browse files
Set default star to output unmapped reads also in the bamfile
parent
a4c324e1
Changes
1
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
cf99b25d
...
...
@@ -98,7 +98,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
/** location of summary file */
def
summaryFile
=
new
File
(
outputDir
,
sampleId
.
getOrElse
(
"x"
)
+
"-"
+
libId
.
getOrElse
(
"x"
)
+
".summary.json"
)
override
def
defaults
=
Map
(
"gsnap"
->
Map
(
"batch"
->
4
))
override
def
defaults
=
Map
(
"gsnap"
->
Map
(
"batch"
->
4
),
"star"
->
Map
(
"outSAMunmapped"
->
"Within"
)
)
override
def
fixedValues
=
Map
(
"gsnap"
->
Map
(
"format"
->
"sam"
),
...
...
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