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biopet.biopet
Commits
e5ac93ab
Commit
e5ac93ab
authored
Nov 23, 2016
by
Sander Bollen
Browse files
style fixes
parent
c3da88c0
Changes
11
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
e5ac93ab
...
...
@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
DepthOfCoverage
(
val
root
:
Configurable
)
extends
CommandLineGATK
{
def
analysis_type
=
"DepthOfCoverage"
...
...
@@ -26,7 +26,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
new
File
(
out
+
"_summary"
)
}
lazy
val
statisticsFile
:
File
=
{
lazy
val
statisticsFile
:
File
=
{
new
File
(
out
+
"_statistics"
)
}
...
...
@@ -117,7 +117,6 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Argument
(
required
=
false
)
var
printBinEndpointsAndExit
:
Boolean
=
false
override
def
cmdLine
=
{
super
.
cmdLine
+
required
(
"--out"
,
out
)
+
optional
(
"--calculateCoverageOverGenes"
,
calculateCoveraOverGenes
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
View file @
e5ac93ab
package
nl.lumc.sasc.biopet.extensions.xhmm
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
/**
* Created by Sander Bollen on 23-11-16.
*
* Generic abstract class for XHMM commands
*/
abstract
class
Xhmm
extends
BiopetCommandLineFunction
with
Version
{
* Created by Sander Bollen on 23-11-16.
*
* Generic abstract class for XHMM commands
*/
abstract
class
Xhmm
extends
BiopetCommandLineFunction
with
Version
{
executable
=
config
(
"exe"
,
namespace
=
"xhmm"
,
default
=
"xhmm"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
View file @
e5ac93ab
...
...
@@ -4,13 +4,13 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.summary.Summarizable
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
scala.io.Source
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmDiscover
(
val
root
:
Configurable
)
extends
Xhmm
with
Summarizable
{
@Input
...
...
@@ -53,7 +53,7 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
map
(
x
=>
XcnvLine
(
x
(
0
),
x
(
1
),
x
(
2
))).
toList
val
samples
=
lines
.
map
(
_
.
sample
)
samples
.
map
{
x
=>
samples
.
map
{
x
=>
val
sampleLines
=
lines
.
filter
(
_
.
sample
==
x
)
x
->
Map
(
"DEL"
->
sampleLines
.
count
(
_
.
cnvType
==
"DEL"
),
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
View file @
e5ac93ab
...
...
@@ -4,11 +4,11 @@ import java.io.File
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmGenotype
(
val
root
:
Configurable
)
extends
Xhmm
with
Reference
{
@Input
...
...
@@ -24,7 +24,7 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
var
r
:
File
=
_
@Argument
var
discoverParamsFile
:
File
=
config
(
"discover_params"
,
namespace
=
"xhmm"
)
var
discoverParamsFile
:
File
=
config
(
"discover_params"
,
namespace
=
"xhmm"
)
def
cmdLine
=
{
executable
+
required
(
"--genotype"
)
+
...
...
@@ -36,6 +36,4 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
required
(
"-v"
,
outputVcf
)
}
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
View file @
e5ac93ab
...
...
@@ -3,12 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmMatrix
(
val
root
:
Configurable
)
extends
Xhmm
{
@Input
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
View file @
e5ac93ab
...
...
@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmMergeGatkDepths
(
val
root
:
Configurable
)
extends
Xhmm
{
@Input
(
doc
=
"List of input depths files"
)
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
View file @
e5ac93ab
...
...
@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmNormalize
(
val
root
:
Configurable
)
extends
Xhmm
{
@Input
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
View file @
e5ac93ab
...
...
@@ -3,11 +3,11 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmPca
(
val
root
:
Configurable
)
extends
Xhmm
{
@Input
...
...
biopet-extensions/src/test/scala/nl/lumc/sasc/biopet/extensions/XhmmTest.scala
View file @
e5ac93ab
...
...
@@ -9,8 +9,8 @@ import org.scalatest.testng.TestNGSuite
import
org.testng.annotations.Test
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmTest
extends
TestNGSuite
with
Matchers
{
@Test
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/Kopisu.scala
View file @
e5ac93ab
...
...
@@ -15,9 +15,9 @@
package
nl.lumc.sasc.biopet.pipelines.kopisu
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.pipelines.kopisu.methods.
{
CnmopsMethod
,
ConiferMethod
,
FreecMethod
,
XhmmMethod
}
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
}
import
nl.lumc.sasc.biopet.pipelines.kopisu.methods.
{
CnmopsMethod
,
ConiferMethod
,
FreecMethod
,
XhmmMethod
}
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -75,7 +75,7 @@ class Kopisu(val root: Configurable) extends QScript with SummaryQScript with Re
add
(
method
)
}
xhmmMethod
.
foreach
{
method
=>
xhmmMethod
.
foreach
{
method
=>
method
.
inputBams
=
inputBams
method
.
outputDir
=
new
File
(
outputDir
,
"xhmm_methid"
)
}
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
e5ac93ab
...
...
@@ -6,8 +6,8 @@ import nl.lumc.sasc.biopet.extensions.xhmm._
import
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by Sander Bollen on 23-11-16.
*/
* Created by Sander Bollen on 23-11-16.
*/
class
XhmmMethod
(
val
root
:
Configurable
)
extends
CnvMethod
with
Reference
{
def
name
=
"xhmm"
...
...
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