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biopet.biopet
Commits
16f4925a
Commit
16f4925a
authored
Jun 24, 2015
by
Peter van 't Hof
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Added bammetrics report to pipeline
parent
95de5080
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18 additions
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3 deletions
+18
-3
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
...nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
+11
-0
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+7
-3
No files found.
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @
16f4925a
...
...
@@ -56,6 +56,17 @@ class BamMetrics(val root: Configurable) extends QScript with SummaryQScript wit
def
summarySettings
=
Map
(
"amplicon_name"
->
ampliconBedFile
.
collect
{
case
x
=>
x
.
getName
.
stripSuffix
(
".bed"
)
},
"roi_name"
->
roiBedFiles
.
map
(
_
.
getName
.
stripSuffix
(
".bed"
)))
override
def
reportClass
=
{
val
bammetricsReport
=
new
BammetricsReport
(
this
)
bammetricsReport
.
outputDir
=
new
File
(
outputDir
,
"report"
)
bammetricsReport
.
summaryFile
=
summaryFile
bammetricsReport
.
args
=
if
(
libId
.
isDefined
)
Map
(
"sampleId"
->
sampleId
.
getOrElse
(
"."
),
"libId"
->
libId
.
getOrElse
(
"."
))
else
Map
(
"sampleId"
->
sampleId
.
getOrElse
(
"."
))
Some
(
bammetricsReport
)
}
/** executed before script */
def
init
()
{
}
...
...
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
16f4925a
...
...
@@ -2,11 +2,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
java.io.
{
PrintWriter
,
File
}
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportBuilder
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.summary.
{
SummaryValue
,
Summary
}
import
nl.lumc.sasc.biopet.extensions.rscript.
{
XYPlot
,
StackedBarPlot
}
//TODO: Add basic report to BamMetrics as single pipeline
class
BammetricsReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
BammetricsReport
}
/**
* Created by pjvan_thof on 3/30/15.
...
...
@@ -54,7 +57,8 @@ object BammetricsReport extends ReportBuilder {
Map
()))),
List
(
"Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
),
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
Map
(
"showPlot"
->
true
))
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
Map
(
"showPlot"
->
true
)),
"Whole genome coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp"
,
Map
(
"showPlot"
->
true
))
),
Map
(
"metricsTag"
->
metricsTag
)
)
...
...
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