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biopet.biopet
Commits
49b6b782
Commit
49b6b782
authored
Nov 07, 2016
by
Peter van 't Hof
Browse files
Switch to lazy error
parent
608c6349
Changes
1
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
View file @
49b6b782
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.delly.DellyCaller
import
nl.lumc.sasc.biopet.extensions.gatk.CatVariants
import
nl.lumc.sasc.biopet.extensions.picard.SortVcf
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caller delly */
...
...
@@ -77,7 +78,7 @@ class Delly(val root: Configurable) extends SvCaller {
catVariants
.
variant
:+=
delly
.
outputvcf
}
require
(
catVariants
.
variant
.
non
Empty
,
"At least 1 SV-type should be selected for Delly"
)
if
(
catVariants
.
variant
.
is
Empty
)
Logging
.
addError
(
"At least 1 SV-type should be selected for Delly"
)
add
(
catVariants
)
...
...
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