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biopet.biopet
Commits
84b4fbf2
Commit
84b4fbf2
authored
Jun 29, 2015
by
bow
Browse files
Set default config for CollectRnaSeqMetrics RefFlat value
parent
9d2bf4ea
Changes
1
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
View file @
84b4fbf2
...
...
@@ -68,7 +68,7 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
var
stopAfter
:
Option
[
Long
]
=
config
(
"stop_after"
)
override
def
beforeGraph
:
Unit
=
{
require
(
refFlat
!
=
null
,
"R
efFlat
file must be supplied.
"
)
if
(
refFlat
=
=
null
)
r
efFlat
=
config
(
"refFlat
"
)
val
validFlags
=
StrandSpecificity
.
values
.
map
(
_
.
toString
).
toSet
strandSpecificity
match
{
case
Some
(
s
)
=>
require
(
validFlags
.
contains
(
s
),
...
...
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