Commit 8263ea12 authored by Ruben Vorderman's avatar Ruben Vorderman
Browse files

FlexiprepReadSummary.ssp defutured

parent 03fa2c53
......@@ -351,9 +351,9 @@ object FlexiprepReadSummaryReportPage {
settings: Map[(Int, Int), Map[String, Option[Any]]],
summary: SummaryDb,
runId: Int
): scala.collection.mutable.Map[Int,scala.collection.mutable.Map[Int,Map[String,Any]]] = {
):scala.collection.mutable.Map[Int,scala.collection.mutable.Map[Int,Map[String,Map[String,Long]]]] = {
var sortableThemeBootstrap = scala.collection.mutable.Map[Int,scala.collection.mutable.Map[Int,Map[String,Any]]]() /* iterable map */
var sortableThemeBootstrap = scala.collection.mutable.Map[Int,scala.collection.mutable.Map[Int,Map[String,Map[String,Long]]]]() /* iterable map */
for (sample <- samples.sortBy(_.name)) {
val sampleRowspan = {
......@@ -377,22 +377,16 @@ object FlexiprepReadSummaryReportPage {
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_total"))
val trimmingStats = summary.getStatKeys(runId, "flexiprep", "trimming_" + read, sample = sample.id, library = lib.id, keyValues = trimmingPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
val clippingDiscardedToShort = clippingStats("num_reads_discarded_too_short").getOrElse(0).toString.toLong
val clippingDiscardedToLong = clippingStats("num_reads_discarded_too_long").getOrElse(0).toString.toLong
val trimmingDiscarded = trimmingStats("num_reads_discarded").getOrElse(0).toString.toLong
val beforeTotal: Long = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal: Long = seqstatQcStats("num_total").getOrElse(0).toString.toLong
val clippingDiscardedTooShort: Long = clippingStats("num_reads_discarded_too_short").getOrElse(0).toString.toLong
val clippingDiscardedTooLong: Long = clippingStats("num_reads_discarded_too_long").getOrElse(0).toString.toLong
val trimmingDiscarded: Long = trimmingStats("num_reads_discarded").getOrElse(0).toString.toLong
sortableThemeBootstrap(sample.id)(lib.id)(read) = Map(
"seqstatPaths" -> seqstatPaths,
"seqstatStats" -> seqstatStats,
"seqstatQcStats" -> seqstatQcStats,
"clippingPaths" -> clippingPaths,
"clippingStats" -> clippingStats,
"trimmingPaths" -> trimmingPaths,
"beforeTotal" -> beforeTotal,
"afterTotal" -> afterTotal,
"clippingDiscardedToShort" -> clippingDiscardedToShort,
"clippingDiscardedToLong" -> clippingDiscardedToLong,
"clippingDiscardedTooShort" -> clippingDiscardedTooShort,
"clippingDiscardedTooLong" -> clippingDiscardedTooLong,
"trimmingDiscarded" -> trimmingDiscarded
)
}
......
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