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biopet.biopet
Commits
3dac3272
Commit
3dac3272
authored
Jun 23, 2015
by
Peter van 't Hof
Browse files
Added wgs histogram
parent
7d824f77
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectWgsMetrics.scala
View file @
3dac3272
...
...
@@ -30,7 +30,7 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
var
minBaseQ
:
Option
[
Int
]
=
config
(
"minimum_base_quality"
)
@Argument
(
doc
=
"COVERAGE_CAP"
,
required
=
false
)
var
covCap
:
Option
[
Int
]
=
config
(
"coverage_cap"
)
var
covCap
:
Option
[
Int
]
=
config
(
"coverage_cap"
,
default
=
401
)
@Argument
(
doc
=
"STOP_AFTER"
,
required
=
false
)
var
stopAfter
:
Option
[
Long
]
=
config
(
"stop_after"
)
...
...
@@ -57,5 +57,8 @@ class CollectWgsMetrics(val root: Configurable) extends Picard with Summarizable
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Map
(
"metrics"
->
Picard
.
getMetrics
(
output
),
"histogram"
->
Picard
.
getHistogram
(
output
)
)
}
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