Commit fc410e94 authored by rhpvorderman's avatar rhpvorderman

Defutured insertsizeplot

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