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Mirrors
biopet.biopet
Commits
72d9f008
Commit
72d9f008
authored
Apr 13, 2015
by
Peter van 't Hof
Browse files
Added insertsize plot
parent
7469830b
Changes
4
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public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
0 → 100644
View file @
72d9f008
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var fields: List[String] = List("All", "Mapped", "Duplicates", "MAPQ>30", "MateUnmapped", "Mate on other chr")%>
<table>
<tbody>
#for (field <- fields)
<tr><th>${field}</th><td>
#if (libId.isDefined)
${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "biopet_flagstat", field)}
#else
${summary.getSampleValue(sampleId.get, metricsTag, "stats", "biopet_flagstat", field)}
#end
</td></tr>
#end
</tbody>
</table>
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/flagstat.ssp
deleted
100644 → 0
View file @
7469830b
#{ //TODO: Need content }#
Todo
\ No newline at end of file
public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
72d9f008
#{ //TODO: Need content }#
#import(nl.lumc.sasc.biopet.core.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("mean_insert_size", "standard_deviation", "median_insert_size")%>
Todo
\ No newline at end of file
#{
def getPlot = {
(if (libId.isDefined) summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "files", "insert_size_metrics", "output_histogram", "path")
else summary.getSampleValue(sampleId.get, metricsTag, "files", "insert_size_metrics", "output_histogram", "path")).collect {
case value => {
val file = new File(value.toString)
val newFile = new File(outputDir, file.getName)
FileUtils.copyFile(file, newFile)
newFile.getName
}
}
}
}#
<iframe src="${getPlot}" style="width:400px; height:400px;" frameborder="0"></iframe>
<table>
<tbody>
#for (field <- fields)
<tr><th>${field}</th><td>
#if (libId.isDefined)
${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "insert_size_metrics", field)}
#else
${summary.getSampleValue(sampleId.get, metricsTag, "stats", "insert_size_metrics", field)}
#end
</td></tr>
#end
</tbody>
</table>
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
72d9f008
...
...
@@ -20,7 +20,7 @@ object BammetricsReport extends ReportBuilder {
Map
(),
List
(
"Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
),
"
Flags
tat"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/
flags
tat.ssp"
),
"
Bam S
tat
s
"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/
bamS
tat
s
.ssp"
),
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
),
"GC Bias"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/gcBias.ssp"
)
),
...
...
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