Commit 09ea599c authored by rhpvorderman's avatar rhpvorderman

Defutured rnaHistogramPlot

parent 505e9ae6
......@@ -478,6 +478,18 @@ object BammetricsReport extends ReportBuilder {
"Whole genome coverage")
}
def rnaHistogramPlotTables(summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Array[Map[String, Array[Any]]] = {
val statsPaths = Map(
"position" -> List("histogram", "normalized_position"),
"count" -> List("histogram", "All_Reads.normalized_coverage")
)
summaryForPlot(summary,statsPaths, "position" :: Nil,
"count" :: Nil, "bammetrics",
"rna",libraryLevel,sampleId,libraryId)
}
/**
* Generate a line plot for rna coverage
*
......@@ -489,30 +501,18 @@ object BammetricsReport extends ReportBuilder {
*/
def rnaHistogramPlot(outputDir: File,
prefix: String,
tables: Array[Map[String, Array[Any]]],
rnaHistogramPlotTables: Array[Map[String, Array[Any]]],
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Unit = {
val statsPaths = Map(
"position" -> List("histogram", "normalized_position"),
"count" -> List("histogram", "All_Reads.normalized_coverage")
)
writePlotFromSummary(
outputDir,
writePlotFromSummary(outputDir,
prefix,
summary,
libraryLevel,
sampleId,
libraryId,
statsPaths,
rnaHistogramPlotTables,
"position" :: Nil,
"count" :: Nil,
"bammetrics",
"rna",
"Relative position",
"Coverage",
"Rna coverage"
"RNA coverage"
)
}
......
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