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biopet.biopet
Commits
bf514e93
Commit
bf514e93
authored
May 04, 2016
by
Peter van 't Hof
Browse files
Remove unused trait
parent
ff0d656a
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/GatkGeneral.scala
deleted
100644 → 0
View file @
ff0d656a
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
nl.lumc.sasc.biopet.core._
import
org.broadinstitute.gatk.engine.phonehome.GATKRunReport
/**
* @deprecated
*/
trait
GatkGeneral
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CommandLineGATK
with
CommandLineResources
with
Reference
with
Version
{
var
executable
:
String
=
config
(
"java"
,
default
=
"java"
,
namespace
=
"java"
,
freeVar
=
false
)
override
def
subPath
=
"gatk"
::
super
.
subPath
jarFile
=
config
(
"gatk_jar"
)
reference_sequence
=
referenceFasta
()
override
def
defaultCoreMemory
=
4.0
override
def
faiRequired
=
true
override
def
dictRequired
=
true
if
(
config
.
contains
(
"intervals"
))
intervals
=
config
(
"intervals"
).
asFileList
if
(
config
.
contains
(
"exclude_intervals"
))
excludeIntervals
=
config
(
"exclude_intervals"
).
asFileList
Option
(
config
(
"et"
).
value
)
match
{
case
Some
(
"NO_ET"
)
=>
et
=
GATKRunReport
.
PhoneHomeOption
.
NO_ET
case
Some
(
"AWS"
)
=>
et
=
GATKRunReport
.
PhoneHomeOption
.
AWS
case
Some
(
"STDOUT"
)
=>
et
=
GATKRunReport
.
PhoneHomeOption
.
STDOUT
case
Some
(
x
)
=>
throw
new
IllegalArgumentException
(
s
"Unknown et option for gatk: $x"
)
case
_
=>
}
if
(
config
.
contains
(
"gatk_key"
))
gatk_key
=
config
(
"gatk_key"
)
if
(
config
.
contains
(
"pedigree"
))
pedigree
=
config
(
"pedigree"
)
def
versionRegex
=
"""(.*)"""
.
r
override
def
versionExitcode
=
List
(
0
,
1
)
def
versionCommand
=
"java"
+
" -jar "
+
jarFile
+
" -version"
override
def
getVersion
=
{
BiopetCommandLineFunction
.
preProcessExecutable
(
executable
).
path
.
foreach
(
executable
=
_
)
super
.
getVersion
.
collect
{
case
v
=>
"Gatk "
+
v
}
}
}
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