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biopet.biopet
Commits
5adb9eea
Commit
5adb9eea
authored
Mar 21, 2017
by
Sander Bollen
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Add wisecondor extensions
parent
3ab8f781
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/Wisecondor.scala
...l/lumc/sasc/biopet/extensions/wisecondor/Wisecondor.scala
+36
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
...c/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
+23
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala
...sc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala
+33
-0
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
.../sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
+27
-0
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/Wisecondor.scala
0 → 100644
View file @
5adb9eea
package
nl.lumc.sasc.biopet.extensions.wisecondor
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Reference
,
Version
}
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
/**
* Created by Sander Bollen on 20-3-17.
*/
abstract
class
Wisecondor
extends
BiopetCommandLineFunction
with
Version
with
Reference
{
executable
=
config
(
"exe"
,
namespace
=
"wisecondor"
,
default
=
"wisecondor"
)
@Input
(
required
=
false
)
var
binFile
:
Option
[
File
]
=
config
(
"bin_file"
,
namespace
=
"wisecondor"
,
default
=
None
)
@Output
var
output
:
File
=
_
// either binSize or binFile must exist
var
binSize
:
Option
[
Int
]
=
config
(
"bin_size"
,
namespace
=
"wisecondor"
,
default
=
None
)
def
binCommand
:
String
=
{
if
(
binFile
.
isDefined
&&
binSize
.
isEmpty
)
{
required
(
"-L"
,
binFile
)
}
else
if
(
binSize
.
isDefined
&&
binFile
.
isEmpty
)
{
required
(
"-B"
,
binSize
)
}
else
{
throw
new
IllegalStateException
(
"bin_file *or* bin_size must be defined"
)
}
}
def
versionCommand
=
executable
+
" --version"
def
versionRegex
=
""".+, version (.*)"""
.
r
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
0 → 100644
View file @
5adb9eea
package
nl.lumc.sasc.biopet.extensions.wisecondor
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by Sander Bollen on 20-3-17.
*/
class
WisecondorCount
(
val
root
:
Configurable
)
extends
Wisecondor
{
@Input
var
inputBam
:
File
=
_
def
cmdLine
=
{
executable
+
required
(
"count"
)
+
required
(
"-I"
,
inputBam
)
+
required
(
"-O"
,
output
)
+
required
(
"-R"
,
referenceFasta
())
+
binCommand
}
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala
0 → 100644
View file @
5adb9eea
package
nl.lumc.sasc.biopet.extensions.wisecondor
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by Sander Bollen on 20-3-17.
*/
class
WisecondorGcCorrect
(
val
root
:
Configurable
)
extends
Wisecondor
{
@Input
var
inputBed
:
File
=
_
var
fracN
:
Option
[
Float
]
=
config
(
"frac_n"
,
namespace
=
"wisecondor"
,
default
=
None
)
var
fracR
:
Option
[
Float
]
=
config
(
"frac_r"
,
namespace
=
"wisecondor"
,
default
=
None
)
var
nIter
:
Option
[
Int
]
=
config
(
"iter"
,
namespace
=
"wisecondor"
,
default
=
None
)
var
fracLowess
:
Option
[
Float
]
=
config
(
"frac_lowess"
,
namespace
=
"wisecondor"
,
default
=
None
)
def
cmdLine
=
{
executable
+
required
(
"gc-correct"
)
+
required
(
"-I"
,
inputBed
)
+
required
(
"-R"
,
referenceFasta
())
+
required
(
"-O"
,
output
)
+
binCommand
+
optional
(
"-n"
,
fracN
)
+
optional
(
"-r"
,
fracR
)
+
optional
(
"-t"
,
nIter
)
+
optional
(
"-l"
,
fracLowess
)
}
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
0 → 100644
View file @
5adb9eea
package
nl.lumc.sasc.biopet.extensions.wisecondor
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by Sander Bollen on 20-3-17.
*/
class
WisecondorZscore
(
val
root
:
Configurable
)
extends
Wisecondor
{
@Input
var
inputBed
:
File
=
_
@Input
var
referenceDictionary
:
File
=
config
(
"reference_dictionary"
,
namespace
=
"wisecondor"
)
def
cmdLine
=
{
executable
+
required
(
"zscore"
)
+
required
(
"-I"
,
inputBed
)
+
required
(
"-O"
,
output
)
+
required
(
"-R"
,
referenceFasta
())
+
required
(
"-D"
,
referenceDictionary
)
+
binCommand
}
}
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