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biopet.biopet
Commits
2052cfc3
Commit
2052cfc3
authored
Nov 28, 2016
by
Sander Bollen
Browse files
autostyle changes
parent
c2087e09
Changes
3
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Side-by-side
biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/XcnvToBed.scala
View file @
2052cfc3
...
...
@@ -4,11 +4,11 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.ToolCommandFunction
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 24-11-16.
*/
* Created by Sander Bollen on 24-11-16.
*/
class
XcnvToBed
(
val
root
:
Configurable
)
extends
ToolCommandFunction
{
def
toolObject
=
nl
.
lumc
.
sasc
.
biopet
.
tools
.
XcnvToBed
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
View file @
2052cfc3
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
}
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
}
import
nl.lumc.sasc.biopet.tools.VepNormalizer.Args
import
nl.lumc.sasc.biopet.utils.ToolCommand
...
...
@@ -8,8 +8,8 @@ import nl.lumc.sasc.biopet.utils.ToolCommand
import
scala.io.Source
/**
* Created by Sander Bollen on 24-11-16.
*/
* Created by Sander Bollen on 24-11-16.
*/
object
XcnvToBed
extends
ToolCommand
{
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
...
...
@@ -17,7 +17,6 @@ object XcnvToBed extends ToolCommand {
.
parse
(
args
,
Args
())
.
getOrElse
(
throw
new
IllegalArgumentException
)
val
writer
=
new
BufferedWriter
(
new
FileWriter
(
commandArgs
.
outputBed
))
Source
.
fromFile
(
commandArgs
.
inputXcnv
).
getLines
().
...
...
@@ -46,7 +45,7 @@ object XcnvToBed extends ToolCommand {
}
}
case
class
Args
(
inputXcnv
:
File
=
null
,
outputBed
:
File
=
null
,
sample
:
String
=
null
)
extends
AbstractArgs
case
class
Args
(
inputXcnv
:
File
=
null
,
outputBed
:
File
=
null
,
sample
:
String
=
null
)
extends
AbstractArgs
class
OptParser
extends
AbstractOptParser
{
head
(
"Convert a sample track within an XHMM XCNV file to a BED track. Fourt column indicates deletion (-1), normal (0) or duplication (1) of region"
)
...
...
@@ -58,12 +57,12 @@ object XcnvToBed extends ToolCommand {
}
text
{
"Input XCNV file"
}
opt
[
File
](
'O'
,
"Output"
)
required
()
valueName
"<bed>"
action
{
(
x
,
c
)
=>
opt
[
File
](
'O'
,
"Output"
)
required
()
valueName
"<bed>"
action
{
(
x
,
c
)
=>
c
.
copy
(
outputBed
=
x
)
}
text
{
"Output BED file"
}
opt
[
String
](
'S'
,
"Sample"
)
required
()
action
{
(
x
,
c
)
=>
opt
[
String
](
'S'
,
"Sample"
)
required
()
action
{
(
x
,
c
)
=>
c
.
copy
(
sample
=
x
)
}
text
{
"The sample which to select"
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
2052cfc3
...
...
@@ -101,7 +101,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
// create bed files
val
bedDir
=
new
File
(
xhmmDir
,
"beds"
)
val
beds
=
inputBams
.
keys
.
map
{
x
=>
val
beds
=
inputBams
.
keys
.
map
{
x
=>
val
z
=
new
XcnvToBed
(
this
)
z
.
inputXcnv
=
discover
.
outputXcnv
z
.
sample
=
x
...
...
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