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biopet.biopet
Commits
5370d60d
Commit
5370d60d
authored
May 03, 2016
by
Peter van 't Hof
Browse files
Fix graph error
parent
613c89ec
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 @
5370d60d
...
...
@@ -111,8 +111,7 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
super
.
freezeFieldValues
()
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
))
if
(!
org
.
broadinstitute
.
gatk
.
utils
.
commandline
.
ArgumentTypeDescriptor
.
isCompressed
(
out
.
getPath
))
outputFiles
:+=
VcfUtils
.
getVcfIndexFile
(
out
)
outputFiles
:+=
VcfUtils
.
getVcfIndexFile
(
out
)
dbsnp
.
foreach
(
VcfUtils
.
getVcfIndexFile
(
_
))
}
...
...
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