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biopet.biopet
Commits
741ab7f5
Commit
741ab7f5
authored
Dec 10, 2016
by
Peter van 't Hof
Browse files
Simplify dbsnp
parent
ba60c6d4
Changes
1
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Inline
Side-by-side
biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
View file @
741ab7f5
...
...
@@ -58,9 +58,9 @@ trait Reference extends Configurable {
}
lazy
val
geneAnnotationVersion
:
Option
[
String
]
=
config
(
"gene_annotation_name"
)
lazy
val
geneAnnotationSubPath
=
geneAnnotationVersion
.
map
(
x
=>
List
(
"gene_annotations"
,
x
)).
getOrElse
(
Nil
)
lazy
val
dbsnpVersion
:
Option
[
Int
]
=
config
(
"dbsnp_version"
)
lazy
val
dbsnpSubPath
:
List
[
String
]
=
dbsnpVersion
.
map
(
x
=>
List
(
"dbsnp_annotations"
,
x
.
toString
)).
getOrElse
(
Nil
)
lazy
val
geneAnnotationSubPath
=
geneAnnotationVersion
.
map
(
List
(
"gene_annotations"
,
_
)).
getOrElse
(
Nil
)
lazy
val
dbsnpVersion
:
Option
[
String
]
=
config
(
"dbsnp_version"
)
lazy
val
dbsnpSubPath
:
List
[
String
]
=
dbsnpVersion
.
map
(
List
(
"dbsnp_annotations"
,
_
)).
getOrElse
(
Nil
)
def
dbsnpVcfFile
:
Option
[
File
]
=
config
(
"dbsnp_vcf"
,
extraSubPath
=
dbsnpSubPath
)
/** Returns the reference config path */
...
...
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