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biopet.biopet
Commits
a952d8c4
Commit
a952d8c4
authored
Sep 22, 2015
by
Peter van 't Hof
Browse files
Convert mapping to sortsam for pipes
parent
9a3356a5
Changes
2
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Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunctionTrait.scala
deleted
100644 → 0
View file @
9a3356a5
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
a952d8c4
...
...
@@ -337,10 +337,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val
sortSam
=
new
SortSam
(
this
)
sortSam
.
output
=
output
if
(
config
(
"use_pipes"
,
default
=
true
).
asBoolean
)
{
val
samtoolsSort
=
new
SamtoolsSort
(
this
)
samtoolsSort
.
outputFormat
=
Some
(
"bam"
)
samtoolsSort
.
output
=
output
add
(
bwaCommand
|
s
amtoolsS
ort
,
chunking
||
!
skipMarkduplicates
)
//
val samtoolsSort = new SamtoolsSort(this)
//
samtoolsSort.outputFormat = Some("bam")
//
samtoolsSort.output = output
add
(
bwaCommand
|
sort
Sam
,
chunking
||
!
skipMarkduplicates
)
}
else
{
bwaCommand
.
output
=
swapExt
(
output
.
getParent
,
output
,
".bam"
,
".sam"
)
add
(
bwaCommand
)
...
...
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