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biopet.biopet
Commits
07d09eb4
Commit
07d09eb4
authored
Sep 09, 2015
by
Peter van 't Hof
Browse files
Style changes
parent
3265843e
Changes
2
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Inline
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/SamplesTsvToJson.scala
View file @
07d09eb4
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
PrintWriter
,
File
}
import
java.io.
{
PrintWriter
,
File
}
import
nl.lumc.sasc.biopet.core.ToolCommand
import
nl.lumc.sasc.biopet.utils.ConfigUtils._
...
...
@@ -30,10 +30,10 @@ object SamplesTsvToJson extends ToolCommand {
case
class
Args
(
inputFiles
:
List
[
File
]
=
Nil
,
outputFile
:
Option
[
File
]
=
None
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
opt
[
File
](
'i'
,
"inputFiles"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'i'
,
"inputFiles"
)
required
()
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
inputFiles
=
x
::
c
.
inputFiles
)
}
text
"Input must be a tsv file, first line is seen as header and must at least have a 'sample' column, 'library' column is optional, multiple files allowed"
opt
[
File
](
'o'
,
"outputFile"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'o'
,
"outputFile"
)
unbounded
()
valueName
"<file>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputFile
=
Some
(
x
))
}
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/utils/VcfUtils.scala
View file @
07d09eb4
...
...
@@ -60,15 +60,15 @@ object VcfUtils {
array
.
foreach
{
case
x
:
Long
=>
out
.
add
(
Long
.
box
(
x
))
case
x
:
Int
=>
out
.
add
(
Int
.
box
(
x
))
case
x
:
Int
=>
out
.
add
(
Int
.
box
(
x
))
case
x
:
Char
=>
out
.
add
(
Char
.
box
(
x
))
case
x
:
Byte
=>
out
.
add
(
Byte
.
box
(
x
))
case
x
:
Double
=>
out
.
add
(
Double
.
box
(
x
))
case
x
:
Float
=>
out
.
add
(
Float
.
box
(
x
))
case
x
:
Boolean
=>
out
.
add
(
Boolean
.
box
(
x
))
case
x
:
String
=>
out
.
add
(
x
)
case
x
:
Object
=>
out
.
add
(
x
)
case
x
=>
out
.
add
(
x
.
toString
)
case
x
:
Float
=>
out
.
add
(
Float
.
box
(
x
))
case
x
:
Boolean
=>
out
.
add
(
Boolean
.
box
(
x
))
case
x
:
String
=>
out
.
add
(
x
)
case
x
:
Object
=>
out
.
add
(
x
)
case
x
=>
out
.
add
(
x
.
toString
)
}
out
}
...
...
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