Commit fb431e6b authored by akaljuvee's avatar akaljuvee

one log line

parent d1017747
......@@ -22,7 +22,7 @@
</tr>
#end
#for (sampleName <- summary.samples)
#for (sampleName <- summary.samples.toList.sorted)
<tr>
<tr>
<td><a href="${rootPath}Samples/${sampleName}/index.html">${sampleName}</a></td>
......
......@@ -8,13 +8,22 @@
<%@ var showIntro: Boolean = true %>
#{
val svTypes = List(("DEL", "Deletion"), ("DUP", "Duplication"), ("INS", "Insertion"), ("INV", "Inversion"))
val svTypes = List(
SvTypeForReport("DEL", "Deletion", "svSummaryDeletions.tsv", "svSummaryDeletions.png"),
SvTypeForReport("DUP", "Duplication", "svSummaryDuplications.tsv", "svSummaryDuplications.png"),
SvTypeForReport("INS", "Insertion", "svSummaryInsertions.tsv", "svSummaryInsertions.png"),
SvTypeForReport("INV", "Inversion", "svSummaryInversions.tsv", "svSummaryInversions.png"))
val counts: Map[String, Map[String, Array[Any]]] = ShivaSvCallingReport.parseSummaryForSvCounts(summary)
ShivaSvCallingReport.writeTsvForPlots(counts, svTypes, outputDir)
ShivaSvCallingReport.createPlots(svTypes, outputDir)
}#
#if (showPlot)
<div class="panel-body">
<img src="svSummary.png" class="img-responsive" />
<img src="svSummaryDeletions.png" class="img-responsive" />
</div>
<div class="panel-footer">
#if (showTable)
......@@ -40,25 +49,25 @@
<th>&gt;10Mb</th>
</tr></thead>
<tbody>
#for (sample <- summary.samples.toList.sorted)
#for (sampleName <- summary.samples.toList.sorted)
#{
val counts:Map[String, Option[Any]] = summary.getSampleValue(sample, "shivasvcalling", "stats", "variantsBySizeAndType").get.asInstanceOf[Map[String, Option[Any]]]
val sampleCounts:Map[String, Array[Any]] = counts.get(sampleName).get
var firstRow = true
}#
#for ((svType, displayLabel) <- svTypes)
#for (sv <- svTypes)
<tr>
#if (counts.contains(svType))
#if (counts.contains(sv.svType))
#if (firstRow)
<td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
<td><a href="${rootPath}Samples/${sampleName}/index.html">${sampleName}</a></td>
#{ firstRow = false }#
#else
<td></td>
#end
<td>${displayLabel}</td>
<td>${sv.displayText}</td>
#for (countForSize <- counts.get(svType).get.asInstanceOf[List[Long]])
#for (countForSize <- counts.get(sv.svType).get.asInstanceOf[List[Long]])
<td>${countForSize}</td>
#end
#end
......
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