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biopet.biopet
Commits
354d418f
Commit
354d418f
authored
Mar 03, 2016
by
Sander Bollen
Browse files
try to parse numeric values as numeric
parent
745b2d24
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
354d418f
...
...
@@ -21,6 +21,7 @@ import nl.lumc.sasc.biopet.core.summary.Summarizable
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
nl.lumc.sasc.biopet.utils.tryToParseNumber
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.io.Source
...
...
@@ -285,8 +286,7 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
if
(
inBlock
)
{
val
key
=
stripped
.
split
(
'\t'
).
head
.
replace
(
" "
,
"_"
)
val
value
=
stripped
.
split
(
'\t'
).
last
theMap
++=
Map
(
key
->
value
)
theMap
++=
Map
(
key
->
tryToParseNumber
(
value
,
fallBack
=
true
).
getOrElse
(
value
))
}
}
if
(
stripped
==
""
)
{
...
...
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