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biopet.biopet
Commits
44731da1
Commit
44731da1
authored
Apr 06, 2016
by
Peter van 't Hof
Browse files
Added more args
parent
5044b1d5
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/BiopetCommandLineFunction.scala
View file @
44731da1
...
...
@@ -165,6 +165,18 @@ trait BiopetCommandLineFunction extends CommandLineResources { biopetFunction =>
this
}
def
multiArg
(
argName
:
String
,
values
:
Iterable
[
Any
],
groupSize
:
Int
=
1
,
minGroups
:
Int
=
0
,
maxGroups
:
Int
=
0
)
:
String
=
{
if
(
values
.
size
%
groupSize
!=
0
)
Logging
.
addError
(
s
"Arg '${argName}' values: '${values}' does not fit to a groupSize of ${groupSize}"
)
val
groups
=
values
.
size
/
groupSize
if
(
groups
<
minGroups
)
Logging
.
addError
(
s
"Args '${argName}' need atleast $minGroups with size $groupSize"
)
if
(
maxGroups
>
0
&&
groups
>
maxGroups
)
Logging
.
addError
(
s
"Args '${argName}' may only have $maxGroups with size $groupSize"
)
if
(
values
.
nonEmpty
)
required
(
argName
)
+
values
.
map
(
required
(
_
)).
mkString
else
""
}
@Output
(
required
=
false
)
private
[
core
]
var
stdoutFile
:
Option
[
File
]
=
None
...
...
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Snptest.scala
View file @
44731da1
...
...
@@ -60,6 +60,41 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
var
conditionOn
:
List
[
String
]
=
config
(
"condition_on"
)
var
priorAdd
:
List
[
String
]
=
config
(
"prior_add"
,
default
=
Nil
)
var
priorCov
:
List
[
String
]
=
config
(
"prior_cov"
,
default
=
Nil
)
var
priorDom
:
List
[
String
]
=
config
(
"prior_dom"
,
default
=
Nil
)
var
priorGen
:
List
[
String
]
=
config
(
"prior_gen"
,
default
=
Nil
)
var
priorHet
:
List
[
String
]
=
config
(
"prior_het"
,
default
=
Nil
)
var
priorRec
:
List
[
String
]
=
config
(
"prior_rec"
,
default
=
Nil
)
var
tDf
:
Option
[
String
]
=
config
(
"t_df"
)
var
tPrior
:
Boolean
=
config
(
"t_prior"
,
default
=
false
)
var
priorMqtQ
:
Option
[
String
]
=
config
(
"prior_mqt_Q"
)
var
priorQtVb
:
Option
[
String
]
=
config
(
"prior_qt_V_b"
)
var
priorQtVq
:
Option
[
String
]
=
config
(
"prior_qt_V_q"
)
var
priorQtA
:
Option
[
String
]
=
config
(
"prior_qt_a"
)
var
priorQtB
:
Option
[
String
]
=
config
(
"prior_qt_b"
)
var
priorQtMeanB
:
Option
[
String
]
=
config
(
"prior_qt_mean_b"
)
var
priorQtMeanQ
:
Option
[
String
]
=
config
(
"prior_qt_mean_q"
)
var
meanBf
:
List
[
String
]
=
config
(
"mean_bf"
,
default
=
Nil
)
var
analysisDescription
:
Option
[
String
]
=
config
(
"analysis_description"
)
var
analysisName
:
Option
[
String
]
=
config
(
"analysis_name"
)
var
chunk
:
Option
[
Int
]
=
config
(
"chunk"
)
var
debug
:
Boolean
=
config
(
"debug"
,
default
=
false
)
var
hwe
:
Boolean
=
config
(
"hwe"
,
default
=
false
)
var
lowerSampleLimit
:
Option
[
Int
]
=
config
(
"lower_sample_limit"
)
var
overlap
:
Boolean
=
config
(
"overlap"
,
default
=
false
)
var
printids
:
Boolean
=
config
(
"printids"
,
default
=
false
)
var
quantileNormalisePhenotypes
:
Boolean
=
config
(
"quantile_normalise_phenotypes"
,
default
=
false
)
var
range
:
List
[
String
]
=
config
(
"range"
,
default
=
Nil
)
var
renorm
:
Boolean
=
config
(
"renorm"
,
default
=
false
)
var
snpid
:
List
[
String
]
=
config
(
"snpid"
,
default
=
Nil
)
var
useRawCovariates
:
Boolean
=
config
(
"use_raw_covariates"
)
var
useRawPhenotypes
:
Boolean
=
config
(
"use_raw_phenotypes"
)
var
noClobber
:
Boolean
=
config
(
"no_clobber"
,
default
=
false
)
executable
=
config
(
"exe"
,
default
=
"snptest"
)
def
versionCommand
:
String
=
executable
+
" -help"
...
...
@@ -70,16 +105,11 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
require
(
inputGenotypes
.
length
==
inputSampleFiles
.
length
)
}
def
multiArg
(
argName
:
String
,
values
:
Iterable
[
Any
])
:
String
=
{
if
(
values
.
nonEmpty
)
required
(
argName
)
+
values
.
map
(
required
(
_
)).
mkString
else
""
}
def
cmdLine
:
String
=
{
val
data
=
inputGenotypes
.
zip
(
inputSampleFiles
).
flatMap
(
x
=>
List
(
x
.
_1
,
x
.
_2
))
required
(
executable
)
+
optional
(
"-assume_chromosome"
,
assumeChromosome
)
+
multiArg
(
"-data"
,
data
)
+
multiArg
(
"-data"
,
data
,
groupSize
=
2
)
+
optional
(
"-genotype_field"
,
genotypeField
)
+
optional
(
"-genotype_probability_scale"
,
genotypeProbabilityScale
)
+
optional
(
"-haploid_genotype_coding"
,
haploidGenotypeCoding
)
+
...
...
@@ -107,7 +137,38 @@ class Snptest(val root: Configurable) extends BiopetCommandLineFunction with Ref
multiArg
(
"-cov_names"
,
covNames
)
+
optional
(
"-sex_column"
,
sexColumn
)
+
optional
(
"-stratify_on"
,
stratifyOn
)
+
multiArg
(
"-condition_on"
,
conditionOn
)
multiArg
(
"-condition_on"
,
conditionOn
)
+
multiArg
(
"-prior_add"
,
priorAdd
,
groupSize
=
4
,
maxGroups
=
1
)
+
multiArg
(
"-prior_cov"
,
priorCov
,
groupSize
=
2
,
maxGroups
=
1
)
+
multiArg
(
"-prior_dom"
,
priorDom
,
groupSize
=
4
,
maxGroups
=
1
)
+
multiArg
(
"-prior_gen"
,
priorGen
,
groupSize
=
6
,
maxGroups
=
1
)
+
multiArg
(
"-prior_het"
,
priorHet
,
groupSize
=
4
,
maxGroups
=
1
)
+
multiArg
(
"-prior_rec"
,
priorRec
,
groupSize
=
4
,
maxGroups
=
1
)
+
optional
(
"-t_df"
,
tDf
)
+
conditional
(
tPrior
,
"-t_prior"
)
+
optional
(
"-prior_mqt_Q"
,
priorMqtQ
)
+
optional
(
"-prior_qt_V_b"
,
priorQtVb
)
+
optional
(
"-prior_qt_V_q"
,
priorQtVq
)
+
optional
(
"-prior_qt_a"
,
priorQtA
)
+
optional
(
"-prior_qt_b"
,
priorQtB
)
+
optional
(
"-prior_qt_mean_b"
,
priorQtMeanB
)
+
optional
(
"-prior_qt_mean_q"
,
priorQtMeanQ
)
+
multiArg
(
"-mean_bf"
,
meanBf
,
groupSize
=
2
,
maxGroups
=
1
)
+
optional
(
"-analysis_description"
,
analysisDescription
)
+
optional
(
"-analysis_name"
,
analysisName
)
+
optional
(
"-chunk"
,
chunk
)
+
conditional
(
debug
,
"-debug"
)
+
conditional
(
hwe
,
"-hwe"
)
+
optional
(
"-lower_sample_limit"
,
lowerSampleLimit
)
+
conditional
(
overlap
,
"-overlap"
)
+
conditional
(
printids
,
"-printids"
)
+
conditional
(
quantileNormalisePhenotypes
,
"quantile_normalise_phenotypes"
)
+
multiArg
(
"-range"
,
range
,
groupSize
=
2
)
+
conditional
(
renorm
,
"-renorm"
)
+
multiArg
(
"-snpid"
,
snpid
)
+
conditional
(
useRawCovariates
,
"-use_raw_covariates"
)
+
conditional
(
useRawPhenotypes
,
"-use_raw_phenotypes"
)
+
conditional
(
noClobber
,
"-no_clobber"
)
}
}
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