From c7b0392c9bf0e73ef85300fb95ffeb62dea41582 Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Thu, 17 Sep 2015 20:15:08 +0200 Subject: [PATCH] Fix plots for library level --- .../pipelines/bammetrics/insertSize.ssp | 2 +- .../pipelines/bammetrics/wgsHistogram.ssp | 2 +- .../bammetrics/BammetricsReport.scala | 22 +++++++++++-------- 3 files changed, 15 insertions(+), 11 deletions(-) diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp index 45f8da529..ba6692dd7 100644 --- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp +++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp @@ -42,7 +42,7 @@ #end #if (showPlot) - #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId) }# + #{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp index 9905a23cf..e900774e0 100644 --- a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp +++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp @@ -36,7 +36,7 @@ #end #if (showPlot) - #{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId) }# + #{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala index f4138e12e..babc43f72 100644 --- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala @@ -156,14 +156,15 @@ object BammetricsReport extends ReportBuilder { prefix: String, summary: Summary, libraryLevel: Boolean = false, - sampleId: Option[String] = None): Unit = { + sampleId: Option[String] = None, + libId: 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.println((for ( sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample; - lib <- summary.libraries(sample) + lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib ) yield s"$sample-$lib") .mkString("library\t", "\t", "")) } else { @@ -198,7 +199,7 @@ object BammetricsReport extends ReportBuilder { if (libraryLevel) { for ( sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample; - lib <- summary.libraries(sample) + lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib ) fill(sample, Some(lib)) } else if (sampleId.isDefined) fill(sampleId.get, None) else summary.samples.foreach(fill(_, None)) @@ -208,7 +209,7 @@ object BammetricsReport extends ReportBuilder { if (libraryLevel) { for ( sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample; - lib <- summary.libraries(sample) + lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib ) tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0")) } else { for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) { @@ -243,14 +244,15 @@ object BammetricsReport extends ReportBuilder { prefix: String, summary: Summary, libraryLevel: Boolean = false, - sampleId: Option[String] = None): Unit = { + sampleId: Option[String] = None, + libId: 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.println((for ( sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample; - lib <- summary.libraries(sample) + lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib ) yield s"$sample-$lib") .mkString("library\t", "\t", "")) } else { @@ -285,7 +287,7 @@ object BammetricsReport extends ReportBuilder { if (libraryLevel) { for ( sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample; - lib <- summary.libraries(sample) + lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib ) fill(sample, Some(lib)) } else if (sampleId.isDefined) fill(sampleId.get, None) else summary.samples.foreach(fill(_, None)) @@ -295,8 +297,10 @@ object BammetricsReport extends ReportBuilder { if (libraryLevel) { for ( sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample; - lib <- summary.libraries(sample) - ) tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0")) + lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib + ) { + tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0")) + } } else { for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) { tsvWriter.print("\t" + counts.getOrElse(sample, "0")) -- GitLab