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biopet.biopet
Commits
67b9334f
Commit
67b9334f
authored
Aug 01, 2017
by
rhpvorderman
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Completely defutured mappingQuality.ssp
parent
10d4ca79
Changes
2
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2 changed files
with
10 additions
and
4 deletions
+10
-4
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
.../lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
+4
-3
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+6
-1
No files found.
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @
67b9334f
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Sample)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema.Library)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
...
...
@@ -19,6 +20,7 @@
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
<%@ var mappingQualityPlotTables: Array[Map[String, Array[Any]]] %>
<%@ var mappingQualityTableResults: Map[(Int, Int), Map[String, Option[Any]]] %>
#{
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
...
...
@@ -87,8 +89,7 @@
#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("mapping_quality", "general", x)).toMap
val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
val results: Map[String, Option[Any]] = mappingQualityTableResults(sample.id, libId)
}#
#for (field <- fields)
<td>${results(field)}</td>
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
67b9334f
...
...
@@ -569,10 +569,11 @@ object BammetricsReport extends ReportBuilder {
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
fields
:
List
[
String
]
=
List
(
"min"
,
"max"
,
"mean"
,
"median"
,
"modal"
),
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
showTable
:
Boolean
=
true
showTable
:
Boolean
=
true
)
:
Map
[
String
,
Any
]
=
{
val
samples
=
sampleId
match
{
...
...
@@ -580,7 +581,11 @@ object BammetricsReport extends ReportBuilder {
case
_
=>
allSamples
.
toList
}
val
mapQualityPlotTables
=
mappingQualityPlotTables
(
summary
,!
sampleLevel
,
sampleId
,
libId
)
val
statsPaths
=
fields
.
map
(
x
=>
x
->
List
(
"mapping_quality"
,
"general"
,
x
)).
toMap
val
mappingQualityTableResults
:
Map
[(
Int
,
Int
)
,
Map
[
String
,
Option
[
Any
]]]
:
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"bamstats"
,
sampleId
,
statsPaths
)
Map
(
"mappingQualityPlotTables"
->
mapQualityPlotTables
,
"mappingQualityTableResults"
->
mappingQualityTableResults
,
"showIntro"
->
showIntro
,
"showTable"
->
showTable
,
"showPlot"
->
showPlot
,
...
...
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