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biopet.biopet
Commits
9605d702
Commit
9605d702
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
fix camelCase names
parent
db06f6bc
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/delly/Delly.scala
View file @
9605d702
...
...
@@ -14,10 +14,10 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
@Input
(
doc
=
"Input file (bam)"
)
var
input
:
File
=
_
var
work
d
ir
:
File
=
_
var
work
D
ir
:
File
=
_
@Output
(
doc
=
"Delly result VCF"
)
var
output
v
cf
:
File
=
_
var
output
V
cf
:
File
=
_
var
outputBaseName
:
File
=
_
...
...
@@ -36,8 +36,8 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
var
outputFiles
:
Map
[
String
,
File
]
=
Map
()
var
vcfFiles
:
Map
[
String
,
File
]
=
Map
()
this
.
outputBaseName
=
work
d
ir
+
input
.
getName
.
substring
(
0
,
input
.
getName
.
lastIndexOf
(
".bam"
))
this
.
output
v
cf
=
outputBaseName
+
".delly.vcf"
this
.
outputBaseName
=
work
D
ir
+
input
.
getName
.
substring
(
0
,
input
.
getName
.
lastIndexOf
(
".bam"
))
this
.
output
V
cf
=
outputBaseName
+
".delly.vcf"
/// start delly and then copy the vcf into the root directory "<sample>.delly/"
if
(
del
)
{
...
...
@@ -79,14 +79,14 @@ class Delly(val root: Configurable) extends QScript with BiopetQScript with Refe
//TODO: convert to biopet extension
val
variants
=
new
CatVariants
()
variants
.
variant
=
vcfFiles
.
values
.
toList
variants
.
outputFile
=
this
.
output
v
cf
variants
.
outputFile
=
this
.
output
V
cf
variants
.
reference
=
referenceFasta
()
// add the job
add
(
variants
)
Some
(
output
v
cf
)
Some
(
output
V
cf
)
}
else
if
(
vcfFiles
.
size
==
1
)
{
// TODO: pretify this
val
ln
=
Ln
(
this
,
vcfFiles
.
head
.
_2
,
this
.
output
v
cf
,
relative
=
true
)
val
ln
=
Ln
(
this
,
vcfFiles
.
head
.
_2
,
this
.
output
V
cf
,
relative
=
true
)
add
(
ln
)
Some
(
ln
.
output
)
}
else
None
...
...
@@ -101,7 +101,7 @@ object Delly extends PipelineCommand {
def
apply
(
root
:
Configurable
,
input
:
File
,
runDir
:
File
)
:
Delly
=
{
val
dellyPipeline
=
new
Delly
(
root
)
dellyPipeline
.
input
=
input
dellyPipeline
.
work
d
ir
=
runDir
dellyPipeline
.
work
D
ir
=
runDir
dellyPipeline
.
init
()
dellyPipeline
.
biopetScript
()
dellyPipeline
...
...
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