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Commit 6f77b5f3 authored by Peter van 't Hof's avatar Peter van 't Hof
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Adding clipping and trimming stats

parent 776769bf
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public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
View file @ 6f77b5f3
......@@ -14,7 +14,8 @@
<th>Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th colspan="2">Discarded</th>
<th>Discarded</th>
<th>(%)</th>
<th>After QC</th>
</tr></thead>
<tbody>
......@@ -38,7 +39,6 @@
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
#{
val beforeTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "bases", "num_total").getOrElse(0).asInstanceOf[Long]
val afterTotal = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "bases", "num_total").getOrElse(0).asInstanceOf[Long]
......
public/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @ 6f77b5f3
......@@ -14,6 +14,8 @@
<th>Sample</th>
<th colspan="2">Library</th>
<th>Before QC</th>
<th>Clipping</th>
<th>Trimming</th>
<th>After QC</th>
</tr></thead>
<tbody>
......@@ -23,7 +25,6 @@
case Some(libId) => List(libId.toString)
case _ => summary.libraries(sample).toList
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
......@@ -37,10 +38,18 @@
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#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 clippingDiscardedToShort = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_short").getOrElse(0).asInstanceOf[Long]
val clippingDiscardedToLong = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "clipping_" + read, "num_reads_discarded_too_long").getOrElse(0).asInstanceOf[Long]
val trimmingDiscarded = summary.getLibraryValue(sample, libId, "flexiprep", "stats", "trimming", "num_reads_discarded_" + read).getOrElse(0).asInstanceOf[Long]
}#
<td>${read}</td>
<td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read, "reads", "num_total")}
</td>
<td> ${summary.getLibraryValue(sample, libId, "flexiprep", "stats", "seqstat_" + read + "_after", "reads", "num_total")}</td>
<td>${beforeTotal}</td>
<td>${clippingDiscardedToShort + clippingDiscardedToLong}</td>
<td>${trimmingDiscarded}</td>
<td>${afterTotal}</td>
#end
</tr>
#end
......
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