Commit ac12d5a9 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed qc stats in report

parent b248300c
......@@ -129,7 +129,7 @@
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "bases", "num_total").getOrElse(0).toString.toLong
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total").getOrElse(0).toString.toLong
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_qc", "bases", "num_total").getOrElse(0).toString.toLong
}#
<td>${read}</td>
<td>${beforeTotal}</td>
......
......@@ -133,7 +133,7 @@
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_qc", "reads", "num_total")
val clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).toString.toLong
val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).toString.toLong
val trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming", "num_reads_discarded_" + read).getOrElse(0).toString.toLong
......
......@@ -95,7 +95,7 @@ object FlexiprepReport extends ReportBuilder {
def getLine(summary: Summary, sample: String, lib: String): String = {
val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "reads", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total"),
val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_qc", "reads", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
val clippingDiscardedToShort = new SummaryValue(List("flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
......@@ -152,7 +152,7 @@ object FlexiprepReport extends ReportBuilder {
def getLine(summary: Summary, sample: String, lib: String): String = {
val beforeTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read, "bases", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total"),
val afterTotal = new SummaryValue(List("flexiprep", "stats", "seqstat_" + read + "_qc", "bases", "num_total"),
summary, Some(sample), Some(lib)).value.getOrElse(0).toString.toLong
val sb = new StringBuffer()
......
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