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biopet.biopet
Commits
f1d14870
Commit
f1d14870
authored
Jun 07, 2017
by
Peter van 't Hof
Browse files
Fixed default
parent
659f81e6
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
View file @
f1d14870
...
...
@@ -46,7 +46,7 @@ class CollectMultipleMetrics(val parent: Configurable)
@Argument
(
doc
=
"Base name of output files"
,
required
=
true
)
var
program
:
List
[
Programs.Value
]
=
{
val
value
:
List
[
String
]
=
config
(
"metrics_programs"
)
val
value
:
List
[
String
]
=
config
(
"metrics_programs"
,
default
=
Nil
)
value
match
{
case
Nil
=>
Programs
.
values
.
toList
case
list
=>
list
.
flatMap
(
x
=>
Programs
.
values
.
find
(
_
.
toString
.
toLowerCase
==
x
.
toLowerCase
))
...
...
@@ -107,17 +107,17 @@ class CollectMultipleMetrics(val parent: Configurable)
summarizable
(
()
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
),
groupBy
=
Some
(
"CATEGORY"
))),
groupBy
=
Some
(
"CATEGORY"
))),
Programs
.
CollectAlignmentSummaryMetrics
.
toString
,
forceSingle
=
true
)
forceSingle
=
true
)
case
Programs
.
CollectInsertSizeMetrics
=>
qscript
.
addSummarizable
(
summarizable
(
()
=>
if
(
new
File
(
outputName
+
".insert_size_metrics"
).
exists
())
Map
(
"metrics"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)),
"metrics"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)),
"histogram"
->
Picard
.
getHistogram
(
new
File
(
outputName
+
".insert_size_metrics"
))
)
...
...
@@ -130,7 +130,8 @@ class CollectMultipleMetrics(val parent: Configurable)
summarizable
(
()
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".quality_distribution_metrics"
))),
Programs
.
QualityScoreDistribution
.
toString
,
forceSingle
=
true
)
forceSingle
=
true
)
case
Programs
.
MeanQualityByCycle
=>
qscript
.
addSummarizable
(
summarizable
(
...
...
@@ -142,9 +143,10 @@ class CollectMultipleMetrics(val parent: Configurable)
summarizable
(
()
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
),
tag
=
"METRICS CLASS"
)),
tag
=
"METRICS CLASS"
)),
Programs
.
CollectBaseDistributionByCycle
.
toString
,
forceSingle
=
true
)
forceSingle
=
true
)
case
_
=>
None
}
}
...
...
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