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biopet.biopet
Commits
b5500137
Commit
b5500137
authored
Nov 18, 2015
by
Sander Bollen
Browse files
Merge branch 'fix-toucan' into 'develop'
Fix toucan See merge request !279
parents
09e0d7e1
80917351
Changes
1
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/VariantEffectPredictor.scala
View file @
b5500137
...
...
@@ -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
}
...
...
@@ -40,8 +41,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
def
versionCommand
=
executable
+
" "
+
vepScript
+
" --help"
//Boolean vars
var
v
:
Boolean
=
config
(
"v"
,
default
=
true
)
var
q
:
Boolean
=
config
(
"q"
,
default
=
false
)
var
v
:
Boolean
=
config
(
"v"
,
default
=
true
,
freeVar
=
false
)
var
q
:
Boolean
=
config
(
"q"
,
default
=
false
,
freeVar
=
false
)
var
offline
:
Boolean
=
config
(
"offline"
,
default
=
false
)
var
no_progress
:
Boolean
=
config
(
"no_progress"
,
default
=
false
)
var
everything
:
Boolean
=
config
(
"everything"
,
default
=
false
)
...
...
@@ -76,8 +77,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var
old_map
:
Boolean
=
config
(
"old_maf"
,
default
=
false
)
var
pubmed
:
Boolean
=
config
(
"pubmed"
,
default
=
false
)
var
vcf
:
Boolean
=
config
(
"vcf"
,
default
=
true
)
var
json
:
Boolean
=
config
(
"json"
,
default
=
false
)
var
vcf
:
Boolean
=
config
(
"vcf"
,
default
=
true
,
freeVar
=
false
)
var
json
:
Boolean
=
config
(
"json"
,
default
=
false
,
freeVar
=
false
)
var
gvf
:
Boolean
=
config
(
"gvf"
,
default
=
false
)
var
check_ref
:
Boolean
=
config
(
"check_ref"
,
default
=
false
)
var
coding_only
:
Boolean
=
config
(
"coding_only"
,
default
=
false
)
...
...
@@ -103,8 +104,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
var
skip_db_check
:
Boolean
=
config
(
"skip_db_check"
,
default
=
false
)
// Textual args
var
vep_config
:
Option
[
String
]
=
config
(
"config"
)
var
species
:
Option
[
String
]
=
config
(
"species"
)
var
vep_config
:
Option
[
String
]
=
config
(
"config"
,
freeVar
=
false
)
var
species
:
Option
[
String
]
=
config
(
"species"
,
freeVar
=
false
)
var
assembly
:
Option
[
String
]
=
config
(
"assembly"
)
var
format
:
Option
[
String
]
=
config
(
"format"
)
var
dir
:
Option
[
String
]
=
config
(
"dir"
)
...
...
@@ -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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