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biopet.biopet
Commits
10d4ca79
Commit
10d4ca79
authored
Jul 31, 2017
by
Ruben Vorderman
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Started defuturing mappingQuality.ssp
parent
a868004e
Changes
3
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3 changed files
with
25 additions
and
26 deletions
+25
-26
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
.../lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
+2
-1
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+22
-24
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+1
-1
No files found.
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @
10d4ca79
...
...
@@ -18,6 +18,7 @@
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var allSamples: Seq[Sample] %>
<%@ var allLibraries: Seq[Library] %>
<%@ var mappingQualityPlotTables: Array[Map[String, Array[Any]]] %>
#{
val samples = sampleId match {
case Some(id) => allSamples.filter(_.id == id).toList
...
...
@@ -43,7 +44,7 @@
#end
#if (showPlot)
#{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality",
summary, !sampleLevel, sampleId = sampleId, libraryId = libId)
}#
#{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality",
mappingQualityPlotTables)
}#
<div class="panel-body">
<img src="mapping_quality.png" class="img-responsive" />
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
10d4ca79
...
...
@@ -17,12 +17,7 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.rscript.
{
LinePlot
,
StackedBarPlot
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
...
...
@@ -534,19 +529,16 @@ object BammetricsReport extends ReportBuilder {
}
writer
.
close
()
}
}
object
BamMetricsAlignmentReport
{
def
values
(
summary
:
SummaryDb
,
runId
:
Int
,
allSamples
:
Seq
[
Sample
],
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
]
=
None
,
libId
:
Option
[
Int
]
=
None
,
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
showTable
:
Boolean
=
true
)
:
Map
[
String
,
Any
]
=
{
def
alignmentReportValues
(
summary
:
SummaryDb
,
runId
:
Int
,
allSamples
:
Seq
[
Sample
],
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
]
=
None
,
libId
:
Option
[
Int
]
=
None
,
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
showTable
:
Boolean
=
true
)
:
Map
[
String
,
Any
]
=
{
val
statsPaths
=
Map
(
"All"
->
List
(
"flagstats"
,
"All"
),
...
...
@@ -571,9 +563,7 @@ object BamMetricsAlignmentReport {
"libId"
->
libId
)
}
}
object
BamMetricsMappingQuality
{
def
values
(
summary
:
SummaryDb
,
def
mappingQualityValues
(
summary
:
SummaryDb
,
runId
:
Int
,
allSamples
:
Seq
[
Sample
],
allLibraries
:
Seq
[
Library
],
...
...
@@ -582,11 +572,19 @@ object BamMetricsMappingQuality {
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
showTable
:
Boolean
=
true
)
:
Map
[
String
,
Any
]
=
{
showTable
:
Boolean
=
true
:
Map
[
String
,
Any
]
=
{
val
samples
=
sampleId
match
{
case
Some
(
id
)
=>
allSamples
.
filter
(
_
.
id
==
id
).
toList
case
_
=>
allSamples
.
toList
}
val
mapQualityPlotTables
=
mappingQualityPlotTables
(
summary
,!
sampleLevel
,
sampleId
,
libId
)
Map
(
"mappingQualityPlotTables"
->
mapQualityPlotTables
,
"showIntro"
->
showIntro
,
"showTable"
->
showTable
,
"showPlot"
->
showPlot
,
"sampleId"
->
sampleId
,
"libId"
->
libId
)
}
}
}
\ No newline at end of file
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
10d4ca79
...
...
@@ -124,7 +124,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
libraries
,
sampleId
,
libId
)
val
alignmentSummary
=
Bam
M
etrics
A
lignmentReport
.
v
alues
(
summary
,
val
alignmentSummary
=
Bam
m
etrics
Report
.
a
lignmentReport
V
alues
(
summary
,
runId
,
samples
,
libraries
,
...
...
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