Commit 3cc33596 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Fix report, the logic to display SE or PE from flexiprep stats is deprecated...

Fix report, the logic to display SE or PE from flexiprep stats is deprecated since we always use flexiprep->cutadapt in SE mode. So only SE mode variables are generated and should be displayed in the report.
parent 778ea9d3
......@@ -144,12 +144,7 @@
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
var trimmingDiscarded: Long = 0
if(paired == true) {
trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming_" + read, "num_reads_discarded_" + read).getOrElse(0).toString.toLong
} else {
trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming_" + read, "num_reads_discarded_total").getOrElse(0).toString.toLong
}
var trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming_" + read, "num_reads_discarded_total").getOrElse(0).toString.toLong
}#
<td>${read}</td>
<td>${beforeTotal}</td>
......
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