Fixed compile issues
| ... | ... | @@ -14,13 +14,17 @@ |
| */ | ||
| package nl.lumc.sasc.biopet.pipelines.shiva | ||
| import java.io.{ File, PrintWriter } | ||
| import java.io.{File, PrintWriter} | ||
| import nl.lumc.sasc.biopet.core.report._ | ||
| import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait | ||
| import nl.lumc.sasc.biopet.utils.config.Configurable | ||
| import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot | ||
| import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue } | ||
| import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb | ||
| import nl.lumc.sasc.biopet.utils.summary.{Summary, SummaryValue} | ||
| import scala.concurrent.Await | ||
| import scala.concurrent.duration.Duration | ||
| /** | ||
| * With this extension the report is executed within a pipeline | ||
| ... | ... | @@ -37,7 +41,8 @@ object ShivaReport extends ShivaReportTrait |
| /** Trait for report generation for Shiva pipeline, this can be extended */ | ||
| trait ShivaReportTrait extends MultisampleMappingReportTrait { | ||
| def variantcallingExecuted = summary.getValue("shiva", "settings", "multisample_variantcalling") match { | ||
| def variantcallingExecuted = summary.getSettingKeys(runId, Right("shiva"), None, keyValues = Map("multisample_variantcalling" -> List("multisample_variantcalling"))).get("multisample_variantcalling") | ||
| .flatten match { | ||
| case Some(true) => true | ||
| case _ => false | ||
| } | ||
| ... | ... | @@ -60,8 +65,8 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait { |
| /** Generate a page with all target coverage stats */ | ||
| def regionsPage: Option[(String, ReportPage)] = { | ||
| val roi = summary.getValue("shiva", "settings", "regions_of_interest") | ||
| val amplicon = summary.getValue("shiva", "settings", "amplicon_bed") | ||
| val roi = summary.getSetting(runId, Right("shiva")).get("regions_of_interest") | ||
| val amplicon = summary.getSetting(runId, Right("shiva")).get("amplicon_bed") | ||
| var regionPages: Map[String, ReportPage] = Map() | ||
| ... | ... | @@ -108,7 +113,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait { |
| } | ||
| /** Single sample page */ | ||
| override def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = { | ||
| override def samplePage(sampleId: Int, args: Map[String, Any]): ReportPage = { | ||
| val variantcallingSection = if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil | ||
| val oldPage = super.samplePage(sampleId, args) | ||
| oldPage.copy(sections = variantcallingSection ++ oldPage.sections) | ||
| ... | ... | @@ -123,51 +128,37 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait { |
| * @param outputDir OutputDir for the tsv and png file | ||
| * @param prefix Prefix of the tsv and png file | ||
| * @param summary Summary class | ||
| * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats | ||
| * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample | ||
| */ | ||
| def variantSummaryPlot(outputDir: File, | ||
| prefix: String, | ||
| summary: Summary, | ||
| libraryLevel: Boolean = false, | ||
| sampleId: Option[String] = None, | ||
| summary: SummaryDb, | ||
| sampleId: Option[Int] = None, | ||
| caller: String = "final", | ||
| target: 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, summarySample: Option[String], lib: Option[String] = None): String = { | ||
| val path = target match { | ||
| case Some(t) => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller-$t", "genotype", sample) | ||
| case _ => List("shivavariantcalling", "stats", s"multisample-vcfstats-$caller", "total", "genotype", "general", sample) | ||
| } | ||
| val homVar = new SummaryValue(path :+ "HomVar", summary, summarySample, lib).value.getOrElse(0).toString.toLong | ||
| val homRef = new SummaryValue(path :+ "HomRef", summary, summarySample, lib).value.getOrElse(0).toString.toLong | ||
| val noCall = new SummaryValue(path :+ "NoCall", summary, summarySample, lib).value.getOrElse(0).toString.toLong | ||
| val het = new SummaryValue(path :+ "Het", summary, summarySample, lib).value.getOrElse(0).toString.toLong | ||
| val sb = new StringBuffer() | ||
| if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t") | ||
| sb.append(homVar + "\t") | ||
| sb.append(het + "\t") | ||
| sb.append(homRef + "\t") | ||
| sb.append(noCall) | ||
| sb.toString | ||
| tsvWriter.print("Sample") | ||
| val field = List("HomVar", "Het", "HomRef", "NoCall") | ||
| tsvWriter.println(s"\t${field.mkString("\t")}") | ||
| val samples = Await.result(summary.getSamples(runId = runId, sampleId = sampleId), Duration.Inf) | ||
| val statsPaths = { | ||
| (for (sample <- Await.result(summary.getSamples(runId = runId), Duration.Inf)) yield { | ||
| field.map(f => s"${sample.name};HomVar" -> List("total", "genotype", "general", sample.name, f)).toMap | ||
| }).fold(Map())(_ ++ _) | ||
| } | ||
| val moduleName = target match { | ||
| case Some(t) => s"multisample-vcfstats-$caller-$t" | ||
| case _ => s"multisample-vcfstats-$caller" | ||
| } | ||
| if (libraryLevel) { | ||
| for ( | ||
| sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get; | ||
| lib <- summary.libraries(sample) | ||
| ) { | ||
| tsvWriter.println(getLine(summary, sample, sampleId, Some(lib))) | ||
| } | ||
| } else { | ||
| for (sample <- summary.samples if sampleId.isEmpty || sample == sampleId.get) { | ||
| tsvWriter.println(getLine(summary, sample, sampleId)) | ||
| } | ||
| val results = summary.getStatKeys(runId, Right("shivavariantcalling"), Some(Right(moduleName)), sampleId.map(Left(_)), keyValues = statsPaths) | ||
| for (sample <- samples if sampleId.isEmpty || sample.id == sampleId.get) { | ||
| tsvWriter.println(sample.name + "\t" + field.map(f => results(s"${sample.name};$f").getOrElse("")).mkString("\t")) | ||
| } | ||
| tsvWriter.close() | ||
| ... | ... | @@ -176,9 +167,7 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait { |
| plot.input = tsvFile | ||
| plot.output = pngFile | ||
| plot.ylabel = Some("VCF records") | ||
| if (libraryLevel) { | ||
| plot.width = Some(200 + (summary.libraries.filter(s => sampleId.getOrElse(s._1) == s._1).foldLeft(0)(_ + _._2.size) * 10)) | ||
| } else plot.width = Some(200 + (summary.samples.count(s => sampleId.getOrElse(s) == s) * 10)) | ||
| </ |