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biopet.biopet
Commits
52e6c553
Commit
52e6c553
authored
Jun 24, 2015
by
Peter van 't Hof
Browse files
Fix reference
parent
4a368a8b
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/BastyGenerateFasta.scala
View file @
52e6c553
...
...
@@ -21,14 +21,14 @@ import htsjdk.variant.variantcontext.VariantContext
import
htsjdk.variant.vcf.VCFFileReader
import
java.io.File
import
java.io.PrintWriter
import
nl.lumc.sasc.biopet.core.
{
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
ToolCommandFuntion
,
BiopetJavaCommandLineFunction
,
ToolCommand
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
scala.collection.JavaConversions._
import
nl.lumc.sasc.biopet.utils.VcfUtils._
import
scala.collection.mutable.ListBuffer
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
{
class
BastyGenerateFasta
(
val
root
:
Configurable
)
extends
ToolCommandFuntion
with
Reference
{
javaMainClass
=
getClass
.
getName
@Input
(
doc
=
"Input vcf file"
,
required
=
false
)
...
...
@@ -38,7 +38,7 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion {
var
bamFile
:
File
=
_
@Input
(
doc
=
"reference"
,
required
=
false
)
var
reference
:
File
=
config
(
"reference"
)
var
reference
:
File
=
_
@Output
(
doc
=
"Output fasta, variants only"
,
required
=
false
)
var
outputVariants
:
File
=
_
...
...
@@ -57,6 +57,11 @@ class BastyGenerateFasta(val root: Configurable) extends ToolCommandFuntion {
override
val
defaultCoreMemory
=
4.0
override
def
beforeGraph
:
Unit
=
{
super
.
beforeGraph
reference
=
referenceFasta
()
}
override
def
commandLine
=
super
.
commandLine
+
optional
(
"--inputVcf"
,
inputVcf
)
+
optional
(
"--bamFile"
,
bamFile
)
+
...
...
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