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biopet.biopet
Commits
68cd247e
Commit
68cd247e
authored
Nov 29, 2016
by
Sander Bollen
Browse files
fix xcnvtobed
parent
7175df93
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
View file @
68cd247e
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
}
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
,
PrintWriter
}
import
nl.lumc.sasc.biopet.tools.VepNormalizer.Args
import
nl.lumc.sasc.biopet.utils.ToolCommand
...
...
@@ -17,14 +17,14 @@ object XcnvToBed extends ToolCommand {
.
parse
(
args
,
Args
())
.
getOrElse
(
throw
new
IllegalArgumentException
)
val
writer
=
new
BufferedWriter
(
new
File
Writer
(
commandArgs
.
outputBed
)
)
val
writer
=
new
Print
Writer
(
commandArgs
.
outputBed
)
Source
.
fromFile
(
commandArgs
.
inputXcnv
).
getLines
().
filter
(!
_
.
startsWith
(
"SAMPLE"
)).
map
(
x
=>
x
.
split
(
"\t"
)).
map
(
x
=>
XcnvBedLine
(
x
(
0
),
x
(
1
),
x
(
2
))).
filter
(
_
.
sample
==
commandArgs
.
sample
).
foreach
(
x
=>
writer
.
w
ri
te
(
x
.
toString
))
foreach
(
x
=>
writer
.
p
ri
ntln
(
x
.
toString
))
writer
.
close
()
}
...
...
@@ -41,7 +41,7 @@ object XcnvToBed extends ToolCommand {
val
chr
=
locs
(
0
)
val
start
=
locs
(
1
).
split
(
"-"
)(
0
)
val
stop
=
locs
(
1
).
split
(
"-"
)(
1
)
s
"$chr\t$start\t$stop\t$cnv
\n
"
s
"$chr\t$start\t$stop\t$cnv"
}
}
...
...
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