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biopet.biopet
Commits
52a36f28
Commit
52a36f28
authored
Feb 14, 2015
by
Peter van 't Hof
Browse files
Fix threads / memlimit
parent
2afb277b
Changes
2
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
View file @
52a36f28
...
...
@@ -41,7 +41,7 @@ class HaplotypeCaller(val root: Configurable) extends org.broadinstitute.gatk.qu
threads
=
1
logger
.
warn
(
"BamOutput is on, nct/threads is forced to set on 1, this option is only for debug"
)
}
nct
=
Some
(
t
hreads
)
nct
=
Some
(
getT
hreads
(
1
)
)
memoryLimit
=
Option
(
memoryLimit
.
getOrElse
(
2.0
)
*
nct
.
getOrElse
(
1
))
}
...
...
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
View file @
52a36f28
...
...
@@ -15,7 +15,7 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
this
.
sample_ploidy
=
config
(
"ploidy"
)
nct
=
config
(
"threads"
,
default
=
1
)
nct
=
Some
(
getThreads
(
1
)
)
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
if
(
config
.
contains
(
"output_mode"
))
{
...
...
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