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biopet.biopet
Commits
4e003490
Commit
4e003490
authored
Dec 14, 2015
by
Peter van 't Hof
Browse files
Fixed args for CollectGcBiasMetrics
parent
3f64deee
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
View file @
4e003490
...
...
@@ -35,7 +35,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
@Output
(
doc
=
"Output chart"
,
required
=
false
)
var
outputChart
:
File
=
_
@Output
(
doc
=
"Output summary"
,
required
=
fals
e
)
@Output
(
doc
=
"Output summary"
,
required
=
tru
e
)
var
outputSummary
:
File
=
_
@Input
(
doc
=
"Reference file"
,
required
=
false
)
...
...
@@ -67,7 +67,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
required
(
"OUTPUT="
,
output
,
spaceSeparated
=
false
)
+
optional
(
"CHART_OUTPUT="
,
outputChart
,
spaceSeparated
=
false
)
+
required
(
"REFERENCE_SEQUENCE="
,
reference
,
spaceSeparated
=
false
)
+
optional
(
"SUMMARY_OUTPUT="
,
outputSummary
,
spaceSeparated
=
false
)
+
required
(
"SUMMARY_OUTPUT="
,
outputSummary
,
spaceSeparated
=
false
)
+
optional
(
"WINDOW_SIZE="
,
windowSize
,
spaceSeparated
=
false
)
+
optional
(
"MINIMUM_GENOME_FRACTION="
,
minGenomeFraction
,
spaceSeparated
=
false
)
+
conditional
(
assumeSorted
,
"ASSUME_SORTED=TRUE"
)
+
...
...
@@ -86,6 +86,7 @@ object CollectGcBiasMetrics {
val
collectGcBiasMetrics
=
new
CollectGcBiasMetrics
(
root
)
collectGcBiasMetrics
.
input
:+=
input
collectGcBiasMetrics
.
output
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".gcbiasmetrics"
)
collectGcBiasMetrics
.
outputSummary
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".gcbiasmetrics.summary"
)
collectGcBiasMetrics
}
}
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