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biopet.biopet
Commit 505e9ae6 authored by Ruben Vorderman's avatar Ruben Vorderman
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Defutured wgsHistogramPlot

parent fc410e94
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Showing with 69 additions and 68 deletions
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ 505e9ae6
......@@ -341,16 +341,15 @@ object BammetricsReport extends ReportBuilder {
"insert_size" -> List("histogram", "insert_size"),
"count" -> List("histogram", "All_Reads.fr_count")
)
val plotTables = summaryForPlot(summary,
statsPaths,
"insert_size" :: Nil,
"count" :: Nil,
"bammetrics",
"CollectInsertSizeMetrics",
libraryLevel,
sampleId,
libraryId)
plotTables
summaryForPlot(summary,
statsPaths,
"insert_size" :: Nil,
"count" :: Nil,
"bammetrics",
"CollectInsertSizeMetrics",
libraryLevel,
sampleId,
libraryId)
}
/**
......@@ -381,16 +380,15 @@ object BammetricsReport extends ReportBuilder {
"mapping_quality" -> List("mapping_quality", "histogram", "values"),
"count" -> List("mapping_quality", "histogram", "counts")
)
val plotTables = summaryForPlot(summary,
statsPaths,
"mapping_quality" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats",
libraryLevel,
sampleId,
libraryId)
plotTables
summaryForPlot(summary,
statsPaths,
"mapping_quality" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats",
libraryLevel,
sampleId,
libraryId)
}
def mappingQualityPlot(outputDir: File,
......@@ -405,37 +403,57 @@ object BammetricsReport extends ReportBuilder {
"Reads",
"Mapping Quality")
}
def clippingPlotTables(summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Array[Map[String, Array[Any]]] = {}
def clippingPlot(outputDir: File,
prefix: String,
clippingPlotTables: Array[Map[String, Array[Any]]],
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Unit = {
libraryId: Option[Int] = None): Array[Map[String, Array[Any]]] = {
val statsPaths = Map(
"clipping" -> List("clipping", "histogram", "values"),
"count" -> List("clipping", "histogram", "counts")
)
summaryForPlot(summary,
statsPaths,
"clipping" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats",
libraryLevel,
sampleId,
libraryId)
writePlotFromSummary(
outputDir,
prefix,
summary,
libraryLevel,
sampleId,
libraryId,
statsPaths,
"clipping" :: Nil,
"count" :: Nil,
"bammetrics",
"bamstats",
"Clipping",
"Reads",
"Clipping"
}
def clippingPlot(outputDir: File,
prefix: String,
clippingPlotTables: Array[Map[String, Array[Any]]]): Unit = {
writePlotFromSummary(outputDir,
prefix,
clippingPlotTables,
"clipping" :: Nil,
"count" :: Nil,
"Clipping",
"Reads",
"Clipping")
}
def wgsHistogramPlotTables(summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Array[Map[String, Array[Any]]] = {
val statsPaths = Map(
"coverage" -> List("histogram", "coverage"),
"count" -> List("histogram", "count"),
"high_quality_coverage_count" -> List("histogram", "high_quality_coverage_count")
)
summaryForPlot(summary,
statsPaths,
"coverage" :: Nil,
"count" :: "high_quality_coverage_count" :: Nil,
"bammetrics",
"wgs",
libraryLevel,
sampleId,
libraryId)
}
/**
......@@ -449,32 +467,15 @@ object BammetricsReport extends ReportBuilder {
*/
def wgsHistogramPlot(outputDir: File,
prefix: String,
tables: Array[Map[String, Array[Any]]],
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None): Unit = {
val statsPaths = Map(
"coverage" -> List("histogram", "coverage"),
"count" -> List("histogram", "count"),
"high_quality_coverage_count" -> List("histogram", "high_quality_coverage_count")
)
writePlotFromSummary(
outputDir,
prefix,
summary,
libraryLevel,
sampleId,
libraryId,
statsPaths,
"coverage" :: Nil,
"count" :: "high_quality_coverage_count" :: Nil,
"bammetrics",
"wgs",
"Coverage",
"Bases",
"Whole genome coverage"
)
wgsHistogramPlotTables: Array[Map[String, Array[Any]]]): Unit = {
writePlotFromSummary(outputDir,
prefix,
wgsHistogramPlotTables,
"coverage" :: Nil,
"count" :: "high_quality_coverage_count" :: Nil,
"Coverage",
"Bases",
"Whole genome coverage")
}
/**
......
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