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biopet.biopet
Commits
90815888
Commit
90815888
authored
Nov 30, 2016
by
Sander Bollen
Browse files
last bits
parent
992d265a
Changes
3
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
90815888
...
...
@@ -3,7 +3,7 @@ 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
,
Input
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
...
...
@@ -44,6 +44,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Output
var
cumulativeCoverageProportionsFile
=
_cumulativeCoverageProportionsFile
@Input
(
required
=
false
)
var
calculateCoverageOverGenes
:
Option
[
File
]
=
config
(
"calculate_coverage_over_genes"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
var
countType
:
Option
[
String
]
=
config
(
"count_type"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
...
...
@@ -126,3 +127,13 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
conditional
(
printBinEndpointsAndExit
,
"--printBinEndPointsAndExit"
)
}
}
object
DepthOfCoverage
{
def
apply
(
root
:
Configurable
,
bamFile
:
List
[
File
],
outFile
:
File
,
targets
:
List
[
File
])
:
DepthOfCoverage
=
{
val
dp
=
new
DepthOfCoverage
(
root
)
dp
.
input_file
=
bamFile
dp
.
intervals
=
targets
dp
.
out
=
outFile
dp
}
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmPca.scala
View file @
90815888
...
...
@@ -13,7 +13,7 @@ class XhmmPca(val root: Configurable) extends Xhmm {
@Input
var
inputMatrix
:
File
=
_
@Output
@Output
(
required
=
true
)
var
pcaFile
:
File
=
_
def
cmdLine
=
{
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
90815888
...
...
@@ -35,7 +35,9 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
}
def
biopetScript
()
=
{
val
depths
=
inputBams
.
map
(
keyValuePair
=>
depthOfCoverage
(
keyValuePair
.
_2
)).
toList
val
depths
=
inputBams
.
map
{
keyValuePair
=>
DepthOfCoverage
(
this
,
List
(
keyValuePair
.
_2
),
swapExt
(
xhmmDir
,
".bam"
,
".dcov"
),
List
(
targets
))
}.
toList
addAll
(
depths
)
// merging of gatk depths files
...
...
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