insertSize.ssp

#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var sampleLevel: Boolean = false %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("mean_insert_size", "standard_deviation", "median_insert_size")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
#{
    val samples = sampleId match {
    case Some(sample) => {
    List(sample.toString)
    }
    case _ => summary.samples.toList
    }
}#

#if (showIntro)
    <br/>
    <div class="row">
    <div class="col-md-1"></div>
    <div class="col-md-6">
        <p>
        #if (sampleId.isDefined && libId.isDefined)
            This plot shows the insert size distribution for all libraries combined in sample <b>${sampleId}</b>.
        #elseif(sampleId.isDefined)
            This plot shows the insert size distribution for the libraries of sample <b>${sampleId}</b>.
        #else
            This plot shows the insert size distribution for each of the <b>${samples.size}</b> samples.
        #end
        <a href="http://thegenomefactory.blogspot.nl/2013/08/paired-end-read-confusion-library.html">Insert size</a> denotes the size of the so-called <em>insert</em> between two read pairs in a paired-end sequencing run. This should correspond to the length of the sequence between the sequencing adaptors. The provided table shows mean and median insert size for each sample, together with the standard deviation.
        </p>
    </div>
    </div>
#end

#if (showPlot)
    #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#

    <div class="panel-body">
    <img src="insertsize.png" class="img-responsive" />
    </div>
    <div class="panel-footer">
        #if (showTable)
            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#insertsizeTable">
                <i class="glyphicon glyphicon-eye-close"></i> Hide table</button>
        #else
            <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#insertsizeTable">
            <i class="glyphicon glyphicon-eye-open"></i> Show table</button>
        #end
      <a href="insertsize.tsv"><button type="button" class="btn btn-info"><i class="glyphicon glyphicon-cloud-download"></i> TSV file</button></a>

    </div>
#end

<div class="panel-body collapse #if (showTable)in#end" id="insertsizeTable">
<!-- Table -->
<table class="table">
    <thead><tr>
        <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
        #if (!sampleLevel) <th>Library</th> #end
        #for (field <- fields)
            <th>${field.replaceAll("_", " ")}</th>
        #end
    </tr></thead>
    <tbody>
        #for (sample <- samples.toList.sorted)
            #{
                val libs = (libId, sampleLevel) match {
                case (_, true) => List("")
                case (Some(libId), _) => List(libId.toString)
                case _ => summary.libraries(sample).toList
                }
            }#
            <tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
            #for (libId <- libs)
                #if (libs.head != libId) <tr> #end
                    #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
                    #{
                        val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")

                        val fieldValues = for (field <- fields) yield {
                            summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse("N/A")
                        }
                    }#
                    #for (value <- fieldValues)
                        <td>${value}</td>
                    #end
                </tr>
            #end
        #end
    </tbody>
</table>

</div>