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biopet.biopet
Commits
6f595a73
Commit
6f595a73
authored
Mar 31, 2017
by
akaljuvee
Browse files
-
parent
c8821092
Changes
1
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
6f595a73
...
...
@@ -15,12 +15,12 @@
package
nl.lumc.sasc.biopet.pipelines.shiva
import
htsjdk.variant.vcf.VCFFileReader
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.Pysvtools
import
nl.lumc.sasc.biopet.pipelines.shiva.svcallers._
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
org.broadinstitute.gatk.queue.QScript
/**
...
...
@@ -152,4 +152,6 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
Map
(
"DEL"
->
delCounts
,
"INS"
->
insCounts
,
"DUP"
->
dupCounts
,
"INV"
->
invCounts
,
"TRA"
->
traCount
)
}
}
\ No newline at end of file
}
object
ShivaSvCalling
extends
PipelineCommand
\ No newline at end of file
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