Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
a8be3036
Commit
a8be3036
authored
May 18, 2015
by
Peter van 't Hof
Browse files
Change stats to histogram
parent
623035b0
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectGcBiasMetrics.scala
View file @
a8be3036
...
...
@@ -71,7 +71,7 @@ class CollectGcBiasMetrics(val root: Configurable) extends Picard with Summariza
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
/** Returns stats for summary */
def
summaryStats
=
Picard
.
get
Metrics
(
output
).
getOrElse
(
Map
()
)
def
summaryStats
=
Picard
.
get
Histogram
(
output
,
tag
=
"METRICS CLASS"
)
}
object
CollectGcBiasMetrics
{
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
View file @
a8be3036
...
...
@@ -81,7 +81,7 @@ class CollectMultipleMetrics(val root: Configurable) extends Picard with Summari
case
_
if
p
==
Programs
.
MeanQualityByCycle
.
toString
=>
Picard
.
getHistogram
(
new
File
(
outputName
+
".quality_by_cycle_metrics"
))
case
_
if
p
==
Programs
.
CollectBaseDistributionByCycle
.
toString
=>
Picard
.
get
Metrics
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
))
Picard
.
get
Histogram
(
new
File
(
outputName
+
".base_distribution_by_cycle_metrics"
)
,
tag
=
"METRICS CLASS"
)
case
_
=>
None
}
val
sum
=
new
Summarizable
{
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment