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biopet.biopet
Commits
7bc8fa62
Commit
7bc8fa62
authored
Nov 23, 2016
by
Sander Bollen
Browse files
depthofcoverage wrapper
parent
a40fb0ff
Changes
1
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
0 → 100644
View file @
7bc8fa62
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Argument
,
Output
}
/**
* Created by Sander Bollen on 23-11-16.
*/
class
DepthOfCoverage
(
val
root
:
Configurable
)
extends
CommandLineGATK
{
def
analysis_type
=
"DepthOfCoverage"
/*
This tool creates several files with `out` as the root
*/
@Output
(
fullName
=
"out"
,
shortName
=
"o"
,
doc
=
"File name base to which coverage metric should be written"
)
var
out
:
String
=
_
lazy
val
outFile
:
File
=
{
new
File
(
out
)
}
lazy
val
summaryFile
:
File
=
{
new
File
(
out
+
"_summary"
)
}
lazy
val
statisticsFile
:
File
=
{
new
File
(
out
+
"_statistics"
)
}
lazy
val
intervalSummaryFile
:
File
=
{
new
File
(
out
+
"_interval_summary"
)
}
lazy
val
intervalStatisticsFile
:
File
=
{
new
File
(
out
+
"_interval_statistics"
)
}
lazy
val
geneSummaryFile
:
File
=
{
new
File
(
out
+
"_gene_summary"
)
}
lazy
val
geneStatisticsFile
:
File
=
{
new
File
(
out
+
"_gene_statistics"
)
}
lazy
val
cumulativeCoverageCountsFile
:
File
=
{
new
File
(
out
+
"_cumulative_coverage_counts"
)
}
lazy
val
cumulativeCoverageProportionsFile
:
File
=
{
new
File
(
out
+
"_cumulative_coverage_proportions"
)
}
@Argument
(
required
=
false
)
var
calculateCoveraOverGenes
:
Option
[
File
]
=
None
@Argument
(
required
=
false
)
var
countType
:
Option
[
String
]
=
None
@Argument
(
required
=
false
)
var
maxBaseQuality
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
maxMappingQuality
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
minBaseQuality
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
minMappingQuality
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
outputFormat
:
Option
[
String
]
=
None
@Argument
(
required
=
false
)
var
partitionType
:
Option
[
String
]
=
None
@Argument
(
required
=
false
)
var
omitDepthOutputAtEachBase
:
Boolean
=
false
@Argument
(
required
=
false
)
var
omitIntervalStatistics
:
Boolean
=
false
@Argument
(
required
=
false
)
var
omitLocusTable
:
Boolean
=
false
@Argument
(
required
=
false
)
var
omitPerSampleStats
:
Boolean
=
false
@Argument
(
required
=
false
)
var
printBaseCounts
:
Boolean
=
false
@Argument
(
required
=
false
)
var
nBins
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
start
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
stop
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
summaryCoverageThreshold
:
Option
[
Int
]
=
None
@Argument
(
required
=
false
)
var
ignoreDeletionSites
:
Boolean
=
false
@Argument
(
required
=
false
)
var
includeDeletions
:
Boolean
=
false
@Argument
(
required
=
false
)
var
includeRefNSites
:
Boolean
=
false
@Argument
(
required
=
false
)
var
printBinEndpointsAndExit
:
Boolean
=
false
override
def
cmdLine
=
{
super
.
cmdLine
+
required
(
"--out"
,
out
)
+
optional
(
"--calculateCoverageOverGenes"
,
calculateCoveraOverGenes
)
+
optional
(
"--countType"
,
countType
)
+
optional
(
"--maxBaseQuality"
,
maxBaseQuality
)
+
optional
(
"--maxMappingQuality"
,
maxMappingQuality
)
+
optional
(
"--minBaseQuality"
,
minBaseQuality
)
+
optional
(
"--minMappingQuality"
,
minMappingQuality
)
+
optional
(
"--outputFormat"
,
outputFormat
)
+
optional
(
"--partitionType"
,
partitionType
)
+
conditional
(
omitDepthOutputAtEachBase
,
"--omitDepthOutputAtEachBase"
)
+
conditional
(
omitIntervalStatistics
,
"--omitIntervalStatistics"
)
+
conditional
(
omitLocusTable
,
"--omitLocusTable"
)
+
conditional
(
omitPerSampleStats
,
"--omitPerSampleStats"
)
+
conditional
(
printBaseCounts
,
"--printBaseCounts"
)
+
optional
(
"--nBins"
,
nBins
)
+
optional
(
"--start"
,
start
)
+
optional
(
"--stop"
,
stop
)
+
optional
(
"--summaryCoverageThreshold"
,
summaryCoverageThreshold
)
+
conditional
(
ignoreDeletionSites
,
"--ignoreDeletionSites"
)
+
conditional
(
includeDeletions
,
"--includeDeletions"
)
+
conditional
(
includeRefNSites
,
"--includeRefNSites"
)
+
conditional
(
printBinEndpointsAndExit
,
"--printBinEndPointsAndExit"
)
}
}
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