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biopet.biopet
Commits
00b8265b
Commit
00b8265b
authored
Aug 18, 2014
by
sajvanderzeeuw
Browse files
Changed one option in BWA.scala so mapping had to be changed as well
parent
f2db87ce
Changes
1
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
00b8265b
...
...
@@ -188,7 +188,7 @@ class Mapping(val root: Configurable) extends QScript with BiopetQScript {
bwaCommand
.
R1
=
R1
if
(
paired
)
bwaCommand
.
R2
=
R2
bwaCommand
.
deps
=
deps
bwaCommand
.
R
G
=
getReadGroup
bwaCommand
.
R
=
getReadGroup
bwaCommand
.
output
=
new
File
(
chunkDir
+
outputName
+
".sam"
)
add
(
bwaCommand
,
isIntermediate
=
true
)
bamFiles
:+=
addSortSam
(
List
(
bwaCommand
.
output
),
swapExt
(
chunkDir
,
bwaCommand
.
output
,
".sam"
,
".bam"
),
chunkDir
)
...
...
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