ShivaReport.scala

package nl.lumc.sasc.biopet.pipelines.shiva

import java.io.{ PrintWriter, File }

import nl.lumc.sasc.biopet.core.config.Configurable
import nl.lumc.sasc.biopet.core.report._
import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary }
import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport

/**
 * Created by pjvan_thof on 3/30/15.
 */
class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
  val builder = ShivaReport
}

object ShivaReport extends MultisampleReportBuilder {

  // FIXME: Not yet finished

  def indexPage = {
    ReportPage(
      Map(
        "Samples" -> generateSamplesPage(pageArgs),
        "Files" -> filesPage,
        "Versions" -> ReportPage(Map(), List(), Map())
      ),
      List(
        "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"),
        "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
          Map("showPlot" -> true, "showTable" -> false)),
        "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
        ),
        "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
          Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
        "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
          Map("showPlot" -> true, "showTable" -> false)),
        "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
          Map("showPlot" -> true, "showTable" -> false))
      ),
      pageArgs
    )
  }

  def filesPage = ReportPage(Map(), List(
    "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
    "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
    "Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp"),
    "Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputBamfiles.ssp"),
    "VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp", Map("sampleId" -> None))
  ), Map())

  def samplePage(sampleId: String, args: Map[String, Any]) = {
    ReportPage(Map(
      "Libraries" -> generateLibraryPage(args),
      "Alignment" -> BammetricsReport.bamMetricsPage,
      "Files" -> filesPage
    ), List(
      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
        if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
      "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
      "Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"),
      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
    ), args)
  }

  def libraryPage(libId: String, args: Map[String, Any]) = {
    ReportPage(Map(
      "Alignment" -> BammetricsReport.bamMetricsPage,
      "QC" -> FlexiprepReport.flexiprepPage
    ), List(
      "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
      "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
      "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
    ), args)
  }

  def reportName = "Shiva Report"

  def variantSummaryPlot(outputDir: File,
                         prefix: String,
                         summary: Summary,
                         libraryLevel: Boolean = false,
                         sampleId: Option[String] = None): Unit = {
    val tsvFile = new File(outputDir, prefix + ".tsv")
    val pngFile = new File(outputDir, prefix + ".png")
    val tsvWriter = new PrintWriter(tsvFile)
    if (libraryLevel) tsvWriter.print("Library") else tsvWriter.print("Sample")
    tsvWriter.println("\tHomVar\tHet\tHomRef\tNoCall")

    def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
      val homVar = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomVar"),
        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
      val homRef = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "HomRef"),
        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
      val noCall = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "NoCall"),
        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
      val het = new SummaryValue(List("shivavariantcalling", "stats", "multisample-vcfstats-final", "genotype", "Het"),
        summary, Some(sample), lib).value.getOrElse(0).toString.toLong
      val sb = new StringBuffer()
      if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
      sb.append(homVar + "\t")
      sb.append(het + "\t")
      sb.append(homRef + "\t")
      sb.append(noCall)
      sb.toString
    }

    if (libraryLevel) {
      for (
        sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get);
        lib <- summary.libraries(sample)
      ) {
        tsvWriter.println(getLine(summary, sample, Some(lib)))
      }
    } else {
      for (sample <- summary.samples if (sampleId.isEmpty || sample == sampleId.get)) {
        tsvWriter.println(getLine(summary, sample))
      }
    }

    tsvWriter.close()

    val plot = new StackedBarPlot(null)
    plot.input = tsvFile
    plot.output = pngFile
    plot.ylabel = Some("VCF records")
    plot.width = Some(1200)
    plot.runLocal()
  }
}