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Commit 03fa2c53 authored by Ruben Vorderman's avatar Ruben Vorderman
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FlexiprepReadSummary.ssp defutured

parent 36b45eb4
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @ 03fa2c53
......@@ -23,11 +23,6 @@
<%-- variables to be added to remove dependency upon futures --%>
<%@ var settings: Map[(Int, Int), Map[String, Option[Any]]] %>
<%@ var paired: Boolean %>
<%@ var seqstatPaths: Map[String, List[String]] %>
<%@ var seqstatStats: Map[String, Option[Any]] %>
<%@ var seqstatQcStats: Map[String, Option[Any]] %>
<%@ var clippingStats: Map[String, Option[Any]] %>
<%@ var trimmingStats: Map[String, Option[Any]] %>
<%@ var samples: Seq[Sample] %>
<%@ var libraries: Seq[Library] %>
<%@ var librariesCount: Int %>
......@@ -35,7 +30,7 @@
<%@ var trimCount: Int %>
<%@ var flexiprepReportPlotRead1: Option[Unit] %>
<%@ var flexiprepReportPlotRead2: Option[Unit] %>
<%@ var sortableThemeBootstrap: scala.collection.mutable.Map[Int,scala.collection.mutable.Map[Int,Map[String,Any]]] %>
<%@ var sortableThemeBootstrap: scala.collection.mutable.Map[Int,scala.collection.mutable.Map[Int,Map[String,Map[String,Long]]]] %>
#if (showIntro)
<br/>
......@@ -149,28 +144,17 @@
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
#{
val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read, sample = sample.id, library = lib.id, keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read + "_qc", sample = sample.id, library = lib.id, keyValues = seqstatPaths)
val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val clippingStats = summary.getStatKeys(runId, "flexiprep", "clipping_" + read, sample = sample.id, library = lib.id, keyValues = clippingPaths)
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 = sortableThemeBootstrap(sample.id)(lib.id)(read)("beforeTotal")
val afterTotal = sortableThemeBootstrap(sample.id)(lib.id)(read)("afterTotal")
val clippingDiscardedTooShort = sortableThemeBootstrap(sample.id)(lib.id)(read)("clippingDiscardedTooShort")
val clippingDiscardedTooLong: Long = sortableThemeBootstrap(sample.id)(lib.id)(read)("clippingDiscardedTooLong")
val trimmingDiscarded: Long = sortableThemeBootstrap(sample.id)(lib.id)(read)("trimmingDiscarded")
}#
<td>${read}</td>
<td>${beforeTotal}</td>
<td>${clippingDiscardedToShort + clippingDiscardedToLong}</td>
<td>${clippingDiscardedTooShort + clippingDiscardedTooLong}</td>
<td>${trimmingDiscarded}</td>
#if (paired == true) <td>${beforeTotal - clippingDiscardedToShort - clippingDiscardedToLong - trimmingDiscarded - afterTotal}</td> #end
#if (paired == true) <td>${beforeTotal - clippingDiscardedTooShort - clippingDiscardedTooLong - trimmingDiscarded - afterTotal}</td> #end
<td>${afterTotal}</td>
#end
</tr>
......
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