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biopet.biopet
Commits
5d9d3661
Commit
5d9d3661
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
fix format
parent
bedfafee
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
View file @
5d9d3661
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
/**
* Created by pjvan_thof on 2/26/15.
...
...
@@ -24,7 +24,7 @@ class CombineVariants(val root: Configurable) extends Gatk {
var
inputMap
:
Map
[
File
,
String
]
=
Map
()
def
addInput
(
file
:
File
,
name
:
String
)
:
Unit
=
{
def
addInput
(
file
:
File
,
name
:
String
)
:
Unit
=
{
inputFiles
:+=
file
inputMap
+=
file
->
name
}
...
...
@@ -40,8 +40,9 @@ class CombineVariants(val root: Configurable) extends Gatk {
(
for
(
file
<-
inputFiles
)
yield
{
inputMap
.
get
(
file
)
match
{
case
Some
(
name
)
=>
required
(
"--variant:"
+
name
,
file
)
case
_
=>
required
(
"--variant"
,
file
)
}}).
mkString
+
case
_
=>
required
(
"--variant"
,
file
)
}
}).
mkString
+
required
(
"-o"
,
outputFile
)
+
optional
(
"--setKey"
,
setKey
)
+
(
if
(
rodPriorityList
.
isEmpty
)
""
else
optional
(
"--rod_priority_list"
,
rodPriorityList
.
mkString
(
","
)))
+
...
...
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