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biopet.biopet
Commits
f70051f1
Commit
f70051f1
authored
Nov 29, 2016
by
Sander Bollen
Browse files
re-arrange auto-generated files from depth of coverage
parent
c5544c76
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/DepthOfCoverage.scala
View file @
f70051f1
...
...
@@ -18,45 +18,31 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Output
(
fullName
=
"out"
,
shortName
=
"o"
,
doc
=
"File name base to which coverage metric should be written"
)
var
out
:
File
=
_
@Output
lazy
val
summaryFile
:
File
=
{
new
File
(
out
+
".sample_summary"
)
}
private
var
_summaryFile
:
File
=
_
private
var
_statisticsFile
:
File
=
_
private
var
_intervalSummaryFile
:
File
=
_
private
var
_intervalStatisticsFile
:
File
=
_
private
var
_geneSummaryFile
:
File
=
_
private
var
_geneStatisticsFile
:
File
=
_
private
var
_cumulativeCoverageCountsFile
:
File
=
_
private
var
_cumulativeCoverageProportionsFile
:
File
=
_
@Output
lazy
val
statisticsFile
:
File
=
{
new
File
(
out
+
".sample_statistics"
)
}
var
summaryFile
=
_summaryFile
@Output
lazy
val
intervalSummaryFile
:
File
=
{
new
File
(
out
+
".sample_interval_summary"
)
}
var
statisticsFile
=
_statisticsFile
@Output
lazy
val
intervalStatisticsFile
:
File
=
{
new
File
(
out
+
".sample_interval_statistics"
)
}
var
intervalSummaryFile
=
_intervalSummaryFile
@Output
lazy
val
geneSummaryFile
:
File
=
{
new
File
(
out
+
".sample_gene_summary"
)
}
var
intervalStatisticsFile
=
_intervalStatisticsFile
@Output
lazy
val
geneStatisticsFile
:
File
=
{
new
File
(
out
+
".sample_gene_statistics"
)
}
var
geneSummaryFile
=
_geneSummaryFile
@Output
lazy
val
cumulativeCoverageCountsFile
:
File
=
{
new
File
(
out
+
".sample_cumulative_coverage_counts"
)
}
var
geneStatisticsFile
=
_geneStatisticsFile
@Output
lazy
va
l
cu
mul
ativeCoverage
ProportionsFile
:
File
=
{
new
File
(
out
+
".sample_cumulative_coverage_proportions"
)
}
va
r
cu
lum
ativeCoverage
CountsFile
=
_cumulativeCoverageCountsFile
@Output
var
cumulativeCoverageProportionsFile
=
_cumulativeCoverageProportionsFile
@Argument
(
required
=
false
)
var
calculateCoveraOverGenes
:
Option
[
File
]
=
None
...
...
@@ -121,6 +107,21 @@ class DepthOfCoverage(val root: Configurable) extends CommandLineGATK {
@Argument
(
required
=
false
)
var
printBinEndpointsAndExit
:
Boolean
=
false
override
def
beforeGraph
()
=
{
super
.
beforeGraph
()
if
(
out
==
null
)
{
throw
new
IllegalStateException
(
"You must set the <out> variable"
)
}
_summaryFile
=
new
File
(
out
+
".sample_summary"
)
_statisticsFile
=
new
File
(
out
+
".sample_statistics"
)
_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"
)
_cumulativeCoverageProportionsFile
=
new
File
(
out
+
".sample_cumulative_coverage_proportions"
)
}
override
def
cmdLine
=
{
super
.
cmdLine
+
required
(
"--out"
,
out
)
+
optional
(
"--calculateCoverageOverGenes"
,
calculateCoveraOverGenes
)
+
...
...
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