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biopet.biopet
Commits
aefd3a63
Commit
aefd3a63
authored
Nov 24, 2015
by
Peter van 't Hof
Browse files
Split into separated files
parent
d97202a8
Changes
4
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
0 → 100644
View file @
aefd3a63
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler Breakdancer */
class
Breakdancer
(
val
root
:
Configurable
)
extends
SvCaller
{
def
name
=
"breakdancer"
def
biopetScript
()
{
//TODO: move minipipeline of breakdancer to here
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
breakdancerDir
=
new
File
(
outputDir
,
sample
)
val
breakdancer
=
Breakdancer
(
this
,
bamFile
,
breakdancerDir
)
addAll
(
breakdancer
.
functions
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
0 → 100644
View file @
aefd3a63
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler Clever */
class
Clever
(
val
root
:
Configurable
)
extends
SvCaller
{
def
name
=
"clever"
def
biopetScript
()
{
//TODO: check double directories
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
cleverDir
=
new
File
(
outputDir
,
sample
)
val
clever
=
CleverCaller
(
this
,
bamFile
,
cleverDir
)
add
(
clever
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
0 → 100644
View file @
aefd3a63
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
nl.lumc.sasc.biopet.extensions.delly.Delly
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Script for sv caler delly */
class
Delly
(
val
root
:
Configurable
)
extends
SvCaller
{
def
name
=
"delly"
def
biopetScript
()
{
//TODO: Move mini delly pipeline to here
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
dellyDir
=
new
File
(
outputDir
,
sample
)
val
delly
=
Delly
(
this
,
bamFile
,
dellyDir
)
delly
.
outputName
=
sample
addAll
(
delly
.
functions
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/SvCaller.scala
View file @
aefd3a63
package
nl.lumc.sasc.biopet.pipelines.shiva.svcallers
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
Reference
,
BiopetQScript
}
import
nl.lumc.sasc.biopet.extensions.breakdancer.Breakdancer
import
nl.lumc.sasc.biopet.extensions.clever.CleverCaller
import
nl.lumc.sasc.biopet.extensions.delly.Delly
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
/**
...
...
@@ -24,44 +18,8 @@ trait SvCaller extends QScript with BiopetQScript with Reference {
def
init
()
=
{}
}
class
Breakdancer
(
val
root
:
Configurable
)
extends
SvCaller
{
def
name
=
"breakdancer"
def
biopetScript
()
{
//TODO: move minipipeline of breakdancer to here
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
breakdancerDir
=
new
File
(
outputDir
,
sample
)
val
breakdancer
=
Breakdancer
(
this
,
bamFile
,
breakdancerDir
)
addAll
(
breakdancer
.
functions
)
}
}
}
/** default mode of bcftools */
class
Clever
(
val
root
:
Configurable
)
extends
SvCaller
{
def
name
=
"clever"
def
biopetScript
()
{
//TODO: check double directories
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
cleverDir
=
new
File
(
outputDir
,
sample
)
val
clever
=
CleverCaller
(
this
,
bamFile
,
cleverDir
)
add
(
clever
)
}
}
}
/** Makes a vcf file from a mpileup without statistics */
class
Delly
(
val
root
:
Configurable
)
extends
SvCaller
{
def
name
=
"delly"
def
biopetScript
()
{
//TODO: Move mini delly pipeline to here
for
((
sample
,
bamFile
)
<-
inputBams
)
{
val
dellyDir
=
new
File
(
outputDir
,
sample
)
val
delly
=
Delly
(
this
,
bamFile
,
dellyDir
)
delly
.
outputName
=
sample
addAll
(
delly
.
functions
)
}
}
}
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