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biopet.biopet
Commits
8a0e0c8e
Commit
8a0e0c8e
authored
Apr 14, 2017
by
Peter van 't Hof
Browse files
Fixing Ln
parent
dd6b452a
Changes
1
Hide whitespace changes
Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMapping.scala
View file @
8a0e0c8e
...
...
@@ -271,7 +271,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
add
(
merge
)
}
add
(
SambambaMarkdup
(
qscript
,
mergedBam
,
bamFile
.
get
,
isIntermediate
=
!
keepMergedFiles
))
Ln
(
qscript
,
bamFile
.
get
+
".bai"
,
bamFile
.
get
.
getAbsolutePath
.
stripSuffix
(
".bam"
)
+
".bai"
)
add
(
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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