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biopet.biopet
Commits
13689911
Commit
13689911
authored
Sep 22, 2015
by
Peter van 't Hof
Browse files
Fix compile errors
parent
bb300878
Changes
2
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public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
13689911
...
...
@@ -38,8 +38,8 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
def
defaultThreads
=
1
var
vmem
:
Option
[
String
]
=
config
(
"vmem"
)
protected
def
defaultCoreMemory
:
Double
=
1.0
protected
def
defaultVmemFactor
:
Double
=
1.4
def
defaultCoreMemory
:
Double
=
1.0
def
defaultVmemFactor
:
Double
=
1.4
var
vmemFactor
:
Double
=
config
(
"vmem_factor"
,
default
=
defaultVmemFactor
)
var
residentFactor
:
Double
=
config
(
"resident_factor"
,
default
=
1.2
)
...
...
@@ -150,13 +150,13 @@ trait BiopetCommandLineFunction extends CommandLineFunction with Configurable {
}
/** Command to get version of executable */
protected
def
versionCommand
:
String
=
null
protected
[
core
]
def
versionCommand
:
String
=
null
/** Regex to get version from version command output */
protected
def
versionRegex
:
Regex
=
null
protected
[
core
]
def
versionRegex
:
Regex
=
null
/** Allowed exit codes for the version command */
protected
def
versionExitcode
=
List
(
0
)
protected
[
core
]
def
versionExitcode
=
List
(
0
)
/** Executes the version command */
private
[
core
]
def
getVersionInternal
:
Option
[
String
]
=
{
...
...
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetJavaCommandLineFunction.scala
View file @
13689911
...
...
@@ -25,7 +25,7 @@ trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetC
javaGCHeapFreeLimit
=
config
(
"java_gc_heap_freelimit"
)
javaGCTimeLimit
=
config
(
"java_gc_timelimit"
)
override
protected
def
defaultVmemFactor
:
Double
=
2.0
override
def
defaultVmemFactor
:
Double
=
2.0
/** Constructs java opts, this adds scala threads */
override
def
javaOpts
=
super
.
javaOpts
+
...
...
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