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biopet.biopet
Commits
b5b9eb61
Commit
b5b9eb61
authored
Nov 17, 2015
by
Peter van 't Hof
Browse files
Changed logging
parent
09e0d7e1
Changes
1
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
b5b9eb61
...
...
@@ -17,6 +17,7 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.utils.Logging
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
Version
,
BiopetCommandLineFunction
,
Reference
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
...
...
@@ -146,9 +147,9 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(!
cache
&&
!
database
)
{
throw
new
IllegalArgumentException
(
"Must supply either cache or database for VariantEffectPredictor"
)
Logging
.
addError
(
"Must supply either cache or database for VariantEffectPredictor"
)
}
else
if
(
cache
&&
dir
.
isEmpty
)
{
throw
new
IllegalArgumentException
(
"Must supply dir to cache for VariantEffectPredictor"
)
Logging
.
addError
(
"Must supply dir to cache for VariantEffectPredictor"
)
}
}
...
...
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