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biopet.biopet
Commits
85f91910
Commit
85f91910
authored
Jun 28, 2015
by
bow
Browse files
Add CollectRnaSeqMetrics histogram to summary file
parent
657d8684
Changes
1
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Inline
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public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectRnaSeqMetrics.scala
View file @
85f91910
...
...
@@ -85,7 +85,9 @@ class CollectRnaSeqMetrics(val root: Configurable) extends Picard with Summariza
"output_chart"
->
chartOutput
).
collect
{
case
(
key
,
Some
(
value
))
=>
key
->
value
}
def
summaryStats
=
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
())
def
summaryStats
=
Map
(
"metrics"
->
Picard
.
getMetrics
(
output
).
getOrElse
(
Map
()),
"histogram"
->
Picard
.
getHistogram
(
output
).
getOrElse
(
Map
()))
override
def
commandLine
=
super
.
commandLine
+
required
(
"INPUT="
,
input
,
spaceSeparated
=
false
)
+
...
...
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