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biopet.biopet
Commits
3eb42a6b
Commit
3eb42a6b
authored
Apr 16, 2015
by
Peter van 't Hof
Browse files
Changed some of the tags for picard summaries
parent
c82a2851
Changes
1
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Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
View file @
3eb42a6b
...
...
@@ -72,16 +72,15 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
case
_
if
p
==
Programs
.
CollectAlignmentSummaryMetrics
.
toString
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
)).
getOrElse
(
Map
())
case
_
if
p
==
Programs
.
CollectInsertSizeMetrics
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)).
getOrElse
(
Map
())
Map
(
"metrics"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)).
getOrElse
(
Map
()),
"histogram"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
),
"HISTOGRAM"
).
getOrElse
(
Map
())
)
case
_
if
p
==
Programs
.
QualityScoreDistribution
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".quality_distribution_metrics"
)).
getOrElse
(
Map
())
Picard
.
getMetrics
(
new
File
(
outputName
+
".quality_distribution_metrics"
),
"HISTOGRAM"
).
getOrElse
(
Map
())
case
_
if
p
==
Programs
.
MeanQualityByCycle
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
)).
getOrElse
(
Map
())
Picard
.
getMetrics
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
),
"HISTOGRAM"
).
getOrElse
(
Map
())
case
_
if
p
==
Programs
.
CollectBaseDistributionByCycle
.
toString
=>
Map
()
Picard
.
getMetrics
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
)).
getOrElse
(
Map
())
case
_
=>
Map
()
}
...
...
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