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biopet.biopet
Commits
2c17add4
Commit
2c17add4
authored
Apr 14, 2017
by
Peter van 't Hof
Browse files
Fixed small issues
parent
2b479c4c
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/sambamba/SambambaMerge.scala
View file @
2c17add4
...
...
@@ -37,6 +37,13 @@ class SambambaMerge(val parent: Configurable) extends Sambamba {
override
def
defaultThreads
=
4
override
def
defaultCoreMemory
=
4.0
@Output
private
var
indexOutput
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
indexOutput
=
new
File
(
output
+
".bai"
)
}
/** Returns command to execute */
def
cmdLine
:
String
=
required
(
executable
)
+
required
(
"merge"
)
+
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
2c17add4
...
...
@@ -267,9 +267,11 @@ trait MultisampleMappingTrait extends MultiSampleQScript
val
merge
=
new
SambambaMerge
(
qscript
)
merge
.
input
=
libraries
.
flatMap
(
_
.
_2
.
preProcessBam
).
toList
merge
.
output
=
mergedBam
merge
.
isIntermediate
=
true
add
(
merge
)
}
add
(
SambambaMarkdup
(
qscript
,
mergedBam
,
bamFile
.
get
,
isIntermediate
=
!
keepMergedFiles
))
Ln
(
qscript
,
bamFile
.
get
+
".bai"
,
bamFile
.
get
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
)
case
_
=>
throw
new
IllegalStateException
(
"This should not be possible, unimplemented MergeStrategy?"
)
}
...
...
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