Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
7175df93
Commit
7175df93
authored
Nov 29, 2016
by
Sander Bollen
Browse files
merge comments on xhmm wrappers
parent
5ef60ac7
Changes
6
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
View file @
7175df93
package
nl.lumc.sasc.biopet.extensions.xhmm
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
/**
* Created by Sander Bollen on 23-11-16.
...
...
@@ -10,6 +12,7 @@ import nl.lumc.sasc.biopet.core.{ BiopetCommandLineFunction, Version }
abstract
class
Xhmm
extends
BiopetCommandLineFunction
with
Version
{
executable
=
config
(
"exe"
,
namespace
=
"xhmm"
,
default
=
"xhmm"
)
var
discoverParamsFile
:
File
=
config
(
"discover_params"
,
namespace
=
"xhmm"
)
def
versionCommand
=
executable
+
" --version"
def
versionRegex
=
"""xhmm (.*)"""
.
r
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmDiscover.scala
View file @
7175df93
...
...
@@ -22,16 +22,21 @@ class XhmmDiscover(val root: Configurable) extends Xhmm with Summarizable {
@Input
var
r
:
File
=
_
@Argument
var
discoverParamsFile
:
File
=
config
(
"discover_params"
,
namespace
=
"xhmm"
)
private
var
_outputXcnvAuxFile
:
File
=
_
private
lazy
val
outputXcnvAuxFile
:
File
=
{
new
File
(
outputXcnv
.
getAbsolutePath
+
".aux"
)
}
@Output
var
outputXcnvAuxFile
=
_outputXcnvAuxFile
@Argument
var
xhmmAnalysisName
:
String
=
_
override
def
beforeGraph
()
=
{
super
.
beforeGraph
()
if
(
outputXcnv
==
null
)
{
throw
new
IllegalStateException
(
"Must set output file"
)
}
_outputXcnvAuxFile
=
new
File
(
outputXcnv
.
getAbsolutePath
+
".aux"
)
}
def
cmdLine
=
{
executable
+
required
(
"--discover"
)
+
required
(
"-r"
,
inputMatrix
)
+
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmGenotype.scala
View file @
7175df93
...
...
@@ -23,8 +23,15 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
@Input
var
r
:
File
=
_
@Argument
var
discoverParamsFile
:
File
=
config
(
"discover_params"
,
namespace
=
"xhmm"
)
@Input
var
f
:
File
=
_
override
def
beforeGraph
()
=
{
super
.
beforeGraph
()
if
(
f
==
null
)
{
f
=
referenceFasta
()
}
}
def
cmdLine
=
{
executable
+
required
(
"--genotype"
)
+
...
...
@@ -32,7 +39,7 @@ class XhmmGenotype(val root: Configurable) extends Xhmm with Reference {
required
(
"-r"
,
inputMatrix
)
+
required
(
"-R"
,
r
)
+
required
(
"-g"
,
inputXcnv
)
+
required
(
"-F"
,
referenceFasta
()
)
+
required
(
"-F"
,
f
)
+
required
(
"-v"
,
outputVcf
)
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMatrix.scala
View file @
7175df93
...
...
@@ -28,37 +28,26 @@ class XhmmMatrix(val root: Configurable) extends Xhmm {
@Input
(
required
=
false
)
var
inputExcludeSamples
:
List
[
File
]
=
Nil
@Argument
var
minTargetSize
:
Int
=
config
(
"min_target_size"
,
namespace
=
"xhmm"
,
default
=
10
)
var
minTargetSize
:
Int
=
config
(
"min_target_size"
,
namespace
=
"xhmm_matrix"
,
default
=
10
)
@Argument
var
maxTargetSize
:
Int
=
config
(
"max_target_size"
,
namespace
=
"xhmm"
,
default
=
10000
)
var
maxTargetSize
:
Int
=
config
(
"max_target_size"
,
namespace
=
"xhmm_matrix"
,
default
=
10000
)
@Argument
var
minMeanTargetRD
:
Int
=
config
(
"min_mean_target_rd"
,
namespace
=
"xhmm"
,
default
=
10
)
var
minMeanTargetRD
:
Int
=
config
(
"min_mean_target_rd"
,
namespace
=
"xhmm_matrix"
,
default
=
10
)
@Argument
var
maxMeanTargetRD
:
Int
=
config
(
"max_mean_target_rd"
,
namespace
=
"xhmm"
,
default
=
500
)
var
maxMeanTargetRD
:
Int
=
config
(
"max_mean_target_rd"
,
namespace
=
"xhmm_matrix"
,
default
=
500
)
@Argument
var
minMeanSampleRD
:
Int
=
config
(
"min_mean_sample_rd"
,
namespace
=
"xhmm"
,
default
=
25
)
var
minMeanSampleRD
:
Int
=
config
(
"min_mean_sample_rd"
,
namespace
=
"xhmm_matrix"
,
default
=
25
)
@Argument
var
maxMeanSampleRD
:
Int
=
config
(
"max_mean_sample_rd"
,
namespace
=
"xhmm"
,
default
=
200
)
var
maxMeanSampleRD
:
Int
=
config
(
"max_mean_sample_rd"
,
namespace
=
"xhmm_matrix"
,
default
=
200
)
@Argument
var
maxSdSampleRD
:
Int
=
config
(
"max_sd_sample_rd"
,
namespace
=
"xhmm"
,
default
=
150
)
var
maxSdSampleRD
:
Int
=
config
(
"max_sd_sample_rd"
,
namespace
=
"xhmm_matrix"
,
default
=
150
)
@Argument
var
maxsdTargetRD
:
Int
=
config
(
"max_sd_target_rd"
,
namespace
=
"xhmm"
,
default
=
30
)
var
maxsdTargetRD
:
Int
=
config
(
"max_sd_target_rd"
,
namespace
=
"xhmm_matrix"
,
default
=
30
)
@Argument
var
centerData
:
Boolean
=
false
@Argument
var
centerType
:
String
=
"sample"
@Argument
var
zScoreData
:
Boolean
=
false
private
def
subCmdLine
=
{
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmMergeGatkDepths.scala
View file @
7175df93
...
...
@@ -17,7 +17,9 @@ class XhmmMergeGatkDepths(val root: Configurable) extends Xhmm {
var
output
:
File
=
_
def
cmdLine
=
{
executable
+
required
(
"--mergeGATKdepths"
)
+
repeat
(
"--GATKdepths"
,
gatkDepthsFiles
)
+
required
(
"-o"
,
output
)
executable
+
required
(
"--mergeGATKdepths"
)
+
repeat
(
"--GATKdepths"
,
gatkDepthsFiles
)
+
required
(
"-o"
,
output
)
}
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/XhmmNormalize.scala
View file @
7175df93
...
...
@@ -19,11 +19,9 @@ class XhmmNormalize(val root: Configurable) extends Xhmm {
@Output
var
normalizeOutput
:
File
=
_
@Argument
var
normalizeMethod
:
String
=
config
(
"normalize_method"
,
namespace
=
"xhmm"
,
default
=
"PVE_mean"
)
var
normalizeMethod
:
String
=
config
(
"normalize_method"
,
namespace
=
"xhmm_normalize"
,
default
=
"PVE_mean"
)
@Argument
var
pveFactor
:
Float
=
config
(
"pve_mean_factor"
,
namespace
=
"xhmm"
,
default
=
0.7
)
var
pveFactor
:
Float
=
config
(
"pve_mean_factor"
,
namespace
=
"xhmm_normalize"
,
default
=
0.7
)
def
cmdLine
=
{
executable
+
required
(
"--normalize"
)
+
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment