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biopet.biopet
Commits
a91e1f83
Commit
a91e1f83
authored
Jul 27, 2015
by
Peter van 't Hof
Browse files
General update of extension
parent
e58842e5
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/clever/CleverCaller.scala
View file @
a91e1f83
...
...
@@ -2,11 +2,11 @@ package nl.lumc.sasc.biopet.extensions.clever
import
java.io.File
import
nl.lumc.sasc.biopet.core.BiopetCommandLineFunction
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetCommandLineFunction
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
class
CleverCaller
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
class
CleverCaller
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
with
Reference
{
executable
=
config
(
"exe"
,
default
=
"clever"
)
private
lazy
val
versionexecutable
:
File
=
config
(
"version_exe"
,
default
=
new
File
(
executable
).
getParent
+
"/ctk-version"
)
...
...
@@ -23,10 +23,8 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
@Input
(
doc
=
"Reference"
)
var
reference
:
File
=
_
@Argument
(
doc
=
"Work directory"
)
var
workDir
:
String
=
_
var
cwd
:
String
=
_
var
workDir
:
File
=
_
var
cwd
:
File
=
_
@Output
(
doc
=
"Clever VCF output"
)
lazy
val
outputvcf
:
File
=
{
...
...
@@ -45,9 +43,10 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
var
k
:
Boolean
=
config
(
"k"
,
default
=
false
)
// keep working directory
var
r
:
Boolean
=
config
(
"r"
,
default
=
false
)
// take read groups into account
override
def
beforeCmd
()
{
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
workDir
==
null
)
throw
new
Exception
(
"Clever :: Workdirectory is not defined"
)
//
if (
input.getName.endsWith(".sort.bam")) sorted = true
if
(
reference
==
null
)
reference
=
referenceFasta
()
}
def
cmdLine
=
required
(
executable
)
+
...
...
@@ -64,10 +63,9 @@ class CleverCaller(val root: Configurable) extends BiopetCommandLineFunction {
}
object
CleverCaller
{
def
apply
(
root
:
Configurable
,
input
:
File
,
reference
:
File
,
svDir
:
String
,
runDir
:
String
)
:
CleverCaller
=
{
def
apply
(
root
:
Configurable
,
input
:
File
,
svDir
:
File
,
runDir
:
File
)
:
CleverCaller
=
{
val
clever
=
new
CleverCaller
(
root
)
clever
.
input
=
input
clever
.
reference
=
reference
clever
.
cwd
=
svDir
clever
.
workDir
=
runDir
clever
...
...
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