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biopet.biopet
Commits
88d51c42
Commit
88d51c42
authored
Jul 16, 2017
by
Peter van 't Hof
Browse files
Adding all Jars
parent
2c2e3865
Changes
1
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biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/vcfstats/VcfStatsSpark.scala
View file @
88d51c42
package
nl.lumc.sasc.biopet.tools.vcfstats
import
java.io.
{
File
,
PrintWriter
}
import
java.net.URLClassLoader
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.tools.vcfstats.VcfStats._
...
...
@@ -124,6 +125,7 @@ object VcfStatsSpark extends ToolCommand {
val
conf
=
new
SparkConf
()
.
setAppName
(
this
.
getClass
.
getSimpleName
)
.
setMaster
(
cmdArgs
.
sparkMaster
.
getOrElse
(
s
"local[${cmdArgs.localThreads}]"
))
.
setJars
(
ClassLoader
.
getSystemClassLoader
.
asInstanceOf
[
URLClassLoader
].
getURLs
.
map
(
_
.
getFile
))
val
sc
=
new
SparkContext
(
conf
)
logger
.
info
(
"Spark context is up"
)
...
...
@@ -183,7 +185,6 @@ object VcfStatsSpark extends ToolCommand {
cmdArgs
.
outputDir
+
"/sample_compare/allele_overlap"
,
samples
)
Thread
.
sleep
(
1000000
)
sc
.
stop
logger
.
info
(
"Done"
)
}
...
...
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