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biopet.biopet
Commits
acf5d263
Commit
acf5d263
authored
Oct 27, 2016
by
Peter van 't Hof
Browse files
Fixed vep config
parent
de951794
Changes
2
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biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/Reference.scala
View file @
acf5d263
...
...
@@ -17,9 +17,9 @@ package nl.lumc.sasc.biopet.core
import
java.io.File
import
htsjdk.samtools.reference.IndexedFastaSequenceFile
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryQScript
,
Summarizable
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
nl.lumc.sasc.biopet.core.summary.
{
Summarizable
,
SummaryQScript
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
LazyCheck
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.
{
Config
,
Configurable
}
import
scala.collection.JavaConversions._
...
...
@@ -59,7 +59,6 @@ trait Reference extends Configurable {
lazy
val
dbsnpVersion
:
Option
[
Int
]
=
config
(
"dbsnp_version"
)
lazy
val
dbsnpSubPath
:
List
[
String
]
=
dbsnpVersion
.
map
(
x
=>
List
(
"dbsnp_annotations"
,
x
.
toString
)).
getOrElse
(
Nil
)
def
dbsnpVcfFile
:
Option
[
File
]
=
config
(
"dbsnp_vcf"
,
extraSubPath
=
dbsnpSubPath
)
lazy
val
vepConfig
:
Option
[
String
]
=
config
(
"vep_config"
)
/** Returns the reference config path */
def
referenceConfigPath
=
{
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
acf5d263
...
...
@@ -17,10 +17,10 @@ package nl.lumc.sasc.biopet.extensions
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.utils.
{
Logging
,
VcfUtils
,
tryToParseNumber
}
import
nl.lumc.sasc.biopet.utils.
{
LazyCheck
,
Logging
,
VcfUtils
,
tryToParseNumber
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.io.Source
...
...
@@ -39,7 +39,15 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
@Output
(
doc
=
"output file"
,
required
=
true
)
var
output
:
File
=
null
override
def
subPath
=
super
.
subPath
++
vepConfig
lazy
val
vepConfig
=
new
LazyCheck
({
val
s
:
Option
[
String
]
=
config
(
"vep_config"
)
s
})
override
def
subPath
=
{
if
(
vepConfig
.
isSet
)
super
.
subPath
++
vepConfig
()
else
super
.
subPath
}
def
versionRegex
=
"""version (\d*)"""
.
r
def
versionCommand
=
executable
+
" "
+
vepScript
+
" --help"
...
...
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