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biopet.biopet
Commits
72896404
Commit
72896404
authored
Mar 23, 2017
by
Peter van 't Hof
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parent
79b33e3a
Changes
4
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4 changed files
with
32 additions
and
37 deletions
+32
-37
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
...c/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
+6
-7
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala
...sc/biopet/extensions/wisecondor/WisecondorGcCorrect.scala
+10
-12
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorNewRef.scala
.../sasc/biopet/extensions/wisecondor/WisecondorNewRef.scala
+9
-10
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
.../sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
+7
-8
No files found.
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorCount.scala
View file @
72896404
...
...
@@ -13,11 +13,10 @@ 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
}
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
View file @
72896404
...
...
@@ -18,16 +18,14 @@ class WisecondorGcCorrect(val root: Configurable) extends Wisecondor {
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
)
}
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/WisecondorNewRef.scala
View file @
72896404
...
...
@@ -6,8 +6,8 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Created by Sander Bollen on 22-3-17.
*/
* Created by Sander Bollen on 22-3-17.
*/
class
WisecondorNewRef
(
val
root
:
Configurable
)
extends
Wisecondor
{
@Input
...
...
@@ -15,13 +15,12 @@ class WisecondorNewRef(val root: Configurable) extends Wisecondor {
var
nNeighbourBins
:
Option
[
Int
]
=
config
(
"n_neighbour_bins"
,
namespace
=
"wisecondor"
,
default
=
None
)
def
cmdLine
=
{
executable
+
required
(
"newref"
)
+
repeat
(
"-I"
,
inputBeds
)
+
required
(
"-O"
,
output
)
+
required
(
"-R"
,
referenceFasta
())
+
binCommand
+
optional
(
"-n"
,
nNeighbourBins
)
}
def
cmdLine
=
executable
+
required
(
"newref"
)
+
repeat
(
"-I"
,
inputBeds
)
+
required
(
"-O"
,
output
)
+
required
(
"-R"
,
referenceFasta
())
+
binCommand
+
optional
(
"-n"
,
nNeighbourBins
)
}
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/wisecondor/WisecondorZscore.scala
View file @
72896404
...
...
@@ -16,12 +16,11 @@ class WisecondorZscore(val root: Configurable) extends Wisecondor {
@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
}
def
cmdLine
=
executable
+
required
(
"zscore"
)
+
required
(
"-I"
,
inputBed
)
+
required
(
"-O"
,
output
)
+
required
(
"-R"
,
referenceFasta
())
+
required
(
"-D"
,
referenceDictionary
)
+
binCommand
}
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