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biopet.biopet
Commits
cb17d470
Commit
cb17d470
authored
Apr 05, 2017
by
Peter van 't Hof
Browse files
Fixing markduplicate dependency
parent
b4cb9bd0
Changes
1
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
cb17d470
...
...
@@ -271,7 +271,7 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
if
(!
skipMarkduplicates
)
{
bamFile
=
new
File
(
outputDir
,
outputName
+
".dedup.bam"
)
val
md
=
MarkDuplicates
(
this
,
bamFiles
,
finalBamFile
)
val
md
=
MarkDuplicates
(
this
,
mergedBamFile
::
Nil
,
finalBamFile
)
md
.
isIntermediate
=
!
keepFinalBamFile
add
(
md
)
addSummarizable
(
md
,
"mark_duplicates"
)
...
...
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