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biopet.biopet
Commits
613e1195
Commit
613e1195
authored
May 04, 2016
by
Peter van 't Hof
Browse files
Fixed graph issue
parent
cf5683e9
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GenotypeGVCFs.scala
View file @
613e1195
...
...
@@ -111,12 +111,16 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
@Gather
(
enabled
=
false
)
private
var
outputIndex
:
File
=
_
override
def
freezeFieldValues
()
{
super
.
freezeFieldValues
()
@Output
@Gather
(
enabled
=
false
)
private
var
dbsnpIndex
:
File
=
_
override
def
beforeGraph
()
{
super
.
beforeGraph
()
deps
++=
variant
.
filter
(
orig
=>
orig
!=
null
&&
(!
orig
.
getName
.
endsWith
(
".list"
))).
map
(
orig
=>
VcfUtils
.
getVcfIndexFile
(
orig
))
if
(
out
!=
null
&&
!
org
.
broadinstitute
.
gatk
.
utils
.
io
.
IOUtils
.
isSpecialFile
(
out
))
outputIndex
=
VcfUtils
.
getVcfIndexFile
(
out
)
dbsnp
.
foreach
(
VcfUtils
.
getVcfIndexFile
(
_
))
dbsnp
.
foreach
(
x
=>
dbsnpIndex
=
VcfUtils
.
getVcfIndexFile
(
x
))
}
override
def
cmdLine
=
super
.
cmdLine
+
...
...
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