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biopet.biopet
Commits
992d265a
Commit
992d265a
authored
Nov 29, 2016
by
Sander Bollen
Browse files
autostyle fixes
parent
134d77a4
Changes
4
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Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
992d265a
...
...
@@ -20,11 +20,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
private
var
_summaryFile
:
File
=
_
private
var
_statisticsFile
:
File
=
_
private
var
_intervalSummaryFile
:
File
=
_
private
var
_intervalSummaryFile
:
File
=
_
private
var
_intervalStatisticsFile
:
File
=
_
private
var
_geneSummaryFile
:
File
=
_
private
var
_geneStatisticsFile
:
File
=
_
private
var
_cumulativeCoverageCountsFile
:
File
=
_
private
var
_cumulativeCoverageCountsFile
:
File
=
_
private
var
_cumulativeCoverageProportionsFile
:
File
=
_
@Output
...
...
@@ -84,7 +84,7 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
var
includeRefNSites
:
Boolean
=
config
(
"include_ref_n_sites"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
var
printBinEndpointsAndExit
:
Boolean
=
config
(
"print_bin_endpoint_and_exit"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
var
printBinEndpointsAndExit
:
Boolean
=
config
(
"print_bin_endpoint_and_exit"
,
namespace
=
"depth_of_coverage"
,
default
=
false
)
override
def
beforeGraph
()
=
{
super
.
beforeGraph
()
...
...
@@ -93,11 +93,11 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
}
_summaryFile
=
new
File
(
out
+
".sample_summary"
)
_statisticsFile
=
new
File
(
out
+
".sample_statistics"
)
_intervalSummaryFile
=
new
File
(
out
+
".sample_interval_summary"
)
_intervalSummaryFile
=
new
File
(
out
+
".sample_interval_summary"
)
_intervalStatisticsFile
=
new
File
(
out
+
".sample_interval_statistics"
)
_geneSummaryFile
=
new
File
(
out
+
".sample_gene_summary"
)
_geneStatisticsFile
=
new
File
(
out
+
".sample_gene_statistics"
)
_cumulativeCoverageCountsFile
=
new
File
(
out
+
".sample_cumulative_coverage_counts"
)
_cumulativeCoverageCountsFile
=
new
File
(
out
+
".sample_cumulative_coverage_counts"
)
_cumulativeCoverageProportionsFile
=
new
File
(
out
+
".sample_cumulative_coverage_proportions"
)
}
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/xhmm/Xhmm.scala
View file @
992d265a
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.extensions.xhmm
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
Version
}
/**
* Created by Sander Bollen on 23-11-16.
...
...
biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/XcnvToBed.scala
View file @
992d265a
package
nl.lumc.sasc.biopet.tools
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
,
PrintWriter
}
import
java.io.
{
BufferedWriter
,
File
,
FileWriter
,
PrintWriter
}
import
nl.lumc.sasc.biopet.tools.VepNormalizer.Args
import
nl.lumc.sasc.biopet.utils.ToolCommand
...
...
kopisu/src/main/scala/nl/lumc/sasc/biopet/pipelines/kopisu/methods/XhmmMethod.scala
View file @
992d265a
...
...
@@ -30,7 +30,7 @@ class XhmmMethod(val root: Configurable) extends CnvMethod with Reference {
"n_bins"
->
200
,
"include_ref_n_sites"
->
true
,
"count_type"
->
"COUNT_FRAGMENTS"
)
)
)
}
...
...
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