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biopet.biopet
Commits
33e49a22
Commit
33e49a22
authored
Nov 24, 2016
by
Peter van 't Hof
Browse files
fix BIOPET-415
parent
85708a4a
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/SortVcf.scala
View file @
33e49a22
...
...
@@ -33,10 +33,15 @@ class SortVcf(val root: Configurable) extends Picard with Reference {
@Input
(
doc
=
"Sequence dictionary to use"
,
required
=
true
)
var
sequenceDictionary
:
File
=
_
@Output
private
var
outputIndex
:
File
=
_
override
val
dictRequired
=
true
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
output
.
getName
.
endsWith
(
".vcf.gz"
))
outputIndex
=
new
File
(
output
.
getAbsolutePath
+
".tbi"
)
if
(
output
.
getName
.
endsWith
(
".vcf"
))
outputIndex
=
new
File
(
output
.
getAbsolutePath
+
".idx"
)
if
(
sequenceDictionary
==
null
)
sequenceDictionary
=
referenceDictFile
}
...
...
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