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biopet.biopet
Commits
bb300878
Commit
bb300878
authored
Sep 22, 2015
by
Peter van 't Hof
Browse files
Moved sam file
parent
4abe2a58
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
bb300878
...
...
@@ -333,7 +333,6 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if
(
paired
)
bwaCommand
.
R2
=
R2
.
get
bwaCommand
.
deps
=
deps
bwaCommand
.
R
=
Some
(
getReadGroupBwa
)
bwaCommand
.
output
=
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".sam"
)
bwaCommand
.
isIntermediate
=
true
if
(
config
(
"use_pipes"
,
default
=
true
).
asBoolean
)
{
val
samtoolsSort
=
new
SamtoolsSort
(
this
)
...
...
@@ -341,6 +340,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
samtoolsSort
.
output
=
output
add
(
bwaCommand
|
samtoolsSort
)
}
else
{
bwaCommand
.
output
=
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".sam"
)
add
(
bwaCommand
)
val
sortSam
=
SortSam
(
this
,
bwaCommand
.
output
,
output
)
if
(
chunking
||
!
skipMarkduplicates
)
sortSam
.
isIntermediate
=
true
...
...
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