Commit fc410e94 authored by rhpvorderman's avatar rhpvorderman

Defutured insertsizeplot

parent dbfdc790
......@@ -342,10 +342,14 @@ object BammetricsReport extends ReportBuilder {
"count" -> List("histogram", "All_Reads.fr_count")
)
val plotTables = summaryForPlot(summary,
statsPaths,
"insert_size" :: Nil,
"count" :: Nil, "bammetrics",
"CollectInsertSizeMetrics",libraryLevel,sampleId,libraryId)
statsPaths,
"insert_size" :: Nil,
"count" :: Nil,
"bammetrics",
"CollectInsertSizeMetrics",
libraryLevel,
sampleId,
libraryId)
plotTables
}
......@@ -359,15 +363,14 @@ object BammetricsReport extends ReportBuilder {
def insertSizePlot(outputDir: File,
prefix: String,
insertSizePlotTables: Array[Map[String, Array[Any]]]): Unit = {
writePlotFromSummary(
outputDir,
prefix,
insertSizePlotTables,
"insert_size" :: Nil,
"count" :: Nil,
"Insert size",
"Reads",
"Insert size")
writePlotFromSummary(outputDir,
prefix,
insertSizePlotTables,
"insert_size" :: Nil,
"count" :: Nil,
"Insert size",
"Reads",
"Insert size")
}
def mappingQualityPlotTables(summary: SummaryDb,
......@@ -379,14 +382,14 @@ object BammetricsReport extends ReportBuilder {
"count" -> List("mapping_quality", "histogram", "counts")
)
val plotTables = summaryForPlot(summary,
statsPaths,
"mapping_quality" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats",
libraryLevel,
sampleId,
libraryId)
statsPaths,
"mapping_quality" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats",
libraryLevel,
sampleId,
libraryId)
plotTables
}
......
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