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biopet.biopet
Commits
cb4cfc7e
Commit
cb4cfc7e
authored
Jul 13, 2017
by
Peter van 't Hof
Browse files
Workaround for making indexes
parent
a0cfa199
Changes
2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/GatherVcfs.scala
View file @
cb4cfc7e
...
...
@@ -16,6 +16,7 @@ package nl.lumc.sasc.biopet.extensions.picard
import
java.io.File
import
nl.lumc.sasc.biopet.extensions.Tabix
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
@@ -27,8 +28,13 @@ class GatherVcfs(val parent: Configurable) extends Picard {
@Output
(
doc
=
"The output file to bam file to"
,
required
=
true
)
var
output
:
File
=
_
override
def
cmdLine
=
val
tabix
:
Option
[
Tabix
]
=
if
(
createIndex
)
Some
(
Tabix
(
this
,
output
))
else
None
override
def
cmdLine
:
String
=
super
.
cmdLine
+
repeat
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
+
(
tabix
match
{
case
Some
(
t
)
=>
s
" && ${t.cmdLine}"
case
_
=>
""
})
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/Picard.scala
View file @
cb4cfc7e
...
...
@@ -50,7 +50,7 @@ abstract class Picard extends BiopetJavaCommandLineFunction with Version {
var
maxRecordsInRam
:
Option
[
Int
]
=
config
(
"maxrecordsinram"
)
@Argument
(
doc
=
"CREATE_INDEX"
,
required
=
false
)
va
r
createIndex
:
Boolean
=
config
(
"createindex"
,
default
=
true
)
va
l
createIndex
:
Boolean
=
config
(
"createindex"
,
default
=
true
)
@Argument
(
doc
=
"CREATE_MD5_FILE"
,
required
=
false
)
var
createMd5
:
Boolean
=
config
(
"createmd5"
,
default
=
false
)
...
...
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