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biopet.biopet
Commits
1865f3b0
Commit
1865f3b0
authored
Feb 16, 2015
by
Peter van 't Hof
Browse files
Added default vmem and add log.file as output file
parent
d125c2f3
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/igvtools/IGVToolsCount.scala
View file @
1865f3b0
...
...
@@ -24,6 +24,9 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
@Output
var
wig
:
Option
[
File
]
=
None
@Output
def
logFile
=
new
File
(
jobLocalDir
,
"igv.log"
)
var
maxZoom
:
Option
[
Int
]
=
config
(
"maxZoom"
)
var
windowSize
:
Option
[
Int
]
=
config
(
"windowSize"
)
var
extFactor
:
Option
[
Int
]
=
config
(
"extFactor"
)
...
...
@@ -41,9 +44,17 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var
pairs
:
Boolean
=
config
(
"pairs"
,
default
=
false
)
override
val
defaultVmem
=
"4G"
override
def
beforeGraph
{
super
.
beforeGraph
(
tdf
,
wig
)
match
{
case
(
Some
(
tdf
),
_
)
=>
jobLocalDir
=
tdf
.
getParentFile
case
(
_
,
Some
(
wig
))
=>
jobLocalDir
=
wig
.
getParentFile
case
_
=>
throw
new
IllegalArgumentException
(
"Must have a wig or tdf file"
)
}
wig
.
foreach
(
x
=>
if
(!
x
.
getAbsolutePath
.
endsWith
(
".wig"
))
throw
new
IllegalArgumentException
(
"WIG file should have a .wig file-extension"
))
tdf
.
foreach
(
x
=>
if
(!
x
.
getAbsolutePath
.
endsWith
(
".tdf"
))
...
...
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