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biopet.biopet
Commits
4f16ffd4
Commit
4f16ffd4
authored
Jul 06, 2017
by
Peter van 't Hof
Browse files
Fix style
parent
687123c6
Changes
1
Hide whitespace changes
Inline
Side-by-side
carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
4f16ffd4
...
...
@@ -54,7 +54,8 @@ class Carp(val parent: Configurable) extends QScript with MultisampleMappingTrai
override
def
makeSample
(
id
:
String
)
=
new
Sample
(
id
)
class
Sample
(
sampleId
:
String
)
extends
super
.
Sample
(
sampleId
)
{
override
def
bamFile
:
Option
[
File
]
=
if
(
libraries
.
size
==
1
)
libraries
.
head
.
_2
.
mapping
.
map
(
_
.
finalBamFile
)
else
super
.
bamFile
override
def
bamFile
:
Option
[
File
]
=
if
(
libraries
.
size
==
1
)
libraries
.
head
.
_2
.
mapping
.
map
(
_
.
finalBamFile
)
else
super
.
bamFile
override
def
preProcessBam
=
Some
(
createFile
(
"filter.bam"
))
...
...
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