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biopet.biopet
Commit 3425ce2f authored by Peter van 't Hof's avatar Peter van 't Hof
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Correct mapping precentage for secondary reads

parent cb93552e
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bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @ 3425ce2f
......@@ -63,6 +63,7 @@
#if (!sampleLevel) <th>Library</th> #end
<th>Total</th>
<th>Mapped</th>
<th>Secondary</th>
<th>(%)</th>
<th>Duplicates</th>
<th>(%)</th>
......@@ -85,10 +86,12 @@
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val secondary = summary.getValue((prefixPath ::: List("biopet_flagstat", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
}#
<td>${total}</td>
<td>${mapped}</td>
<td>${mapped.toDouble / total * 100}%</td>
<td>${secondary}</td>
<td>${(mapped - secondary).toDouble / (total - secondary) * 100}%</td>
<td>${duplicates}</td>
<td>${duplicates.toDouble / total * 100}%</td>
</tr>
......
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