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biopet.biopet
Commits
c3e801d4
Commit
c3e801d4
authored
Jul 13, 2017
by
Peter van 't Hof
Browse files
Workaround for index creation
parent
cb4cfc7e
Changes
1
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Inline
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherVcfs.scala
View file @
c3e801d4
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.extensions.Tabix
import
nl.lumc.sasc.biopet.utils.VcfUtils
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
@@ -28,7 +29,16 @@ class GatherVcfs(val parent: Configurable) extends Picard {
@Output
(
doc
=
"The output file to bam file to"
,
required
=
true
)
var
output
:
File
=
_
val
tabix
:
Option
[
Tabix
]
=
if
(
createIndex
)
Some
(
Tabix
(
this
,
output
))
else
None
//FIXME: This is a workaround for this issue: https://github.com/broadinstitute/picard/issues/789
def
tabix
:
Option
[
Tabix
]
=
if
(
createIndex
)
Some
(
Tabix
(
this
,
output
))
else
None
@Output
(
required
=
false
)
private
var
index
:
File
=
_
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
createIndex
)
index
=
VcfUtils
.
getVcfIndexFile
(
output
)
}
override
def
cmdLine
:
String
=
super
.
cmdLine
+
...
...
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