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biopet.biopet
Commits
5ef60ac7
Commit
5ef60ac7
authored
Nov 29, 2016
by
Sander Bollen
Browse files
config values for all arguments
parent
f70051f1
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
5ef60ac7
...
...
@@ -44,68 +44,47 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Output
var
cumulativeCoverageProportionsFile
=
_cumulativeCoverageProportionsFile
@Argument
(
required
=
false
)
var
calculateCoveraOverGenes
:
Option
[
File
]
=
None
var
calculateCoverageOverGenes
:
Option
[
File
]
=
config
(
"calculate_coverage_over_genes"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
countType
:
Option
[
String
]
=
None
var
countType
:
Option
[
String
]
=
config
(
"count_type"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
maxBaseQuality
:
Option
[
Int
]
=
None
var
maxBaseQuality
:
Option
[
Int
]
=
config
(
"max_base_quality"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
maxMappingQuality
:
Option
[
Int
]
=
None
var
maxMappingQuality
:
Option
[
Int
]
=
config
(
"max_mapping_quality"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
minBaseQuality
:
Option
[
Int
]
=
None
var
minBaseQuality
:
Option
[
Int
]
=
config
(
"min_base_quality"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
minMappingQuality
:
Option
[
Int
]
=
None
var
minMappingQuality
:
Option
[
Int
]
=
config
(
"min_mapping_quality"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
outputFormat
:
Option
[
String
]
=
None
var
outputFormat
:
Option
[
String
]
=
config
(
"output_format"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
partitionType
:
Option
[
String
]
=
None
var
partitionType
:
Option
[
String
]
=
config
(
"partition_type"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
omitDepthOutputAtEachBase
:
Boolean
=
false
var
omitDepthOutputAtEachBase
:
Boolean
=
config
(
"omit_depth_output_at_each_base"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
omitIntervalStatistics
:
Boolean
=
false
var
omitIntervalStatistics
:
Boolean
=
config
(
"omit_interval_statistics"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
omitLocusTable
:
Boolean
=
false
var
omitLocusTable
:
Boolean
=
config
(
"omit_locus_table"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
omitPerSampleStats
:
Boolean
=
false
var
omitPerSampleStats
:
Boolean
=
config
(
"omit_per_sample_stats"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
printBaseCounts
:
Boolean
=
false
var
printBaseCounts
:
Boolean
=
config
(
"print_base_counts"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
nBins
:
Option
[
Int
]
=
None
var
nBins
:
Option
[
Int
]
=
config
(
"n_bins"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
start
:
Option
[
Int
]
=
None
var
start
:
Option
[
Int
]
=
config
(
"start"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
stop
:
Option
[
Int
]
=
None
var
stop
:
Option
[
Int
]
=
config
(
"stop"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
summaryCoverageThreshold
:
Option
[
Int
]
=
None
var
summaryCoverageThreshold
:
Option
[
Int
]
=
config
(
"summary_coverage_threshold"
,
namespace
=
"depth_of_coverage"
,
default
=
None
)
@Argument
(
required
=
false
)
var
ignoreDeletionSites
:
Boolean
=
false
var
ignoreDeletionSites
:
Boolean
=
config
(
"ignore_deletion_sites"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
includeDeletions
:
Boolean
=
false
var
includeDeletions
:
Boolean
=
config
(
"include_deletions"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
includeRefNSites
:
Boolean
=
false
var
includeRefNSites
:
Boolean
=
config
(
"include_RefNSites"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
@Argument
(
required
=
false
)
var
printBinEndpointsAndExit
:
Boolean
=
false
var
printBinEndpointsAndExit
:
Boolean
=
config
(
"print_bin_endpoint_and_exit"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
override
def
beforeGraph
()
=
{
super
.
beforeGraph
()
...
...
@@ -124,7 +103,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
override
def
cmdLine
=
{
super
.
cmdLine
+
required
(
"--out"
,
out
)
+
optional
(
"--calculateCoverageOverGenes"
,
calculateCoveraOverGenes
)
+
optional
(
"--calculateCoverageOverGenes"
,
calculateCovera
ge
OverGenes
)
+
optional
(
"--countType"
,
countType
)
+
optional
(
"--maxBaseQuality"
,
maxBaseQuality
)
+
optional
(
"--maxMappingQuality"
,
maxMappingQuality
)
+
...
...
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