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biopet.biopet
Commits
a085648e
Commit
a085648e
authored
Mar 14, 2017
by
Peter van 't Hof
Browse files
Fixing BIOPET-612
parent
9170ed43
Changes
2
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bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @
a085648e
...
...
@@ -74,7 +74,7 @@
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("metrics", x)).toMap
val statsPaths = fields.map(x => x -> List("metrics", x
.toUpperCase
)).toMap
val results = summary.getStatKeys(runId, "bammetrics", "wgs", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}#
#for (field <- fields)
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
a085648e
...
...
@@ -286,8 +286,8 @@ object BammetricsReport extends ReportBuilder {
sampleId
:
Option
[
Int
]
=
None
,
libraryId
:
Option
[
Int
]
=
None
)
:
Unit
=
{
val
statsPaths
=
Map
(
"coverage"
->
List
(
"wgs"
,
"histogram"
,
"coverage"
),
"count"
->
List
(
"wgs"
,
"histogram"
,
"count"
)
"coverage"
->
List
(
"histogram"
,
"coverage"
),
"count"
->
List
(
"histogram"
,
"count"
)
)
writePlotFromSummary
(
outputDir
,
prefix
,
summary
,
libraryLevel
,
sampleId
,
libraryId
,
statsPaths
,
...
...
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