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biopet.biopet
Commits
d6fcf3f9
Commit
d6fcf3f9
authored
Apr 04, 2016
by
Peter van 't Hof
Browse files
Fixed files
parent
ab7420cc
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
d6fcf3f9
...
...
@@ -474,11 +474,11 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val
zcatR1
=
extractIfNeeded
(
R1
,
output
.
getParentFile
)
val
zcatR2
=
if
(
paired
)
Some
(
extractIfNeeded
(
R2
.
get
,
output
.
getParentFile
))
else
None
val
starCommand
=
Star
(
this
,
zcatR1
.
_2
,
zcatR2
.
map
(
_
.
_2
),
outputDir
,
isIntermediate
=
true
)
val
ar
=
addAddOrReplaceReadGroups
(
starCommand
.
outputSam
,
output
)
val
ar
=
addAddOrReplaceReadGroups
(
starCommand
.
outputSam
,
swapExt
(
outputDir
,
output
,
".bam"
,
".addAddOrReplaceReadGroups.bam"
)
)
val
reorderSam
=
new
ReorderSam
(
this
)
reorderSam
.
input
=
ar
.
_2
reorderSam
.
output
=
swapExt
(
ar
.
_2
.
getParentFile
,
output
,
".bam"
,
".reordered.bam"
)
reorderSam
.
output
=
output
val
pipe
=
new
BiopetFifoPipe
(
this
,
(
zcatR1
.
_1
::
(
if
(
paired
)
zcatR2
.
get
.
_1
else
None
)
::
Some
(
starCommand
)
::
Some
(
ar
.
_1
)
::
Some
(
reorderSam
)
::
Nil
).
flatten
)
...
...
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