Commit 99c245a2 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixed report of Carp

parent 346fcbff
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport) #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File) #import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %> <%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %> <%@ var libId: Option[Int] = None %>
...@@ -89,7 +89,7 @@ ...@@ -89,7 +89,7 @@
"Duplicates" -> List("flagstats", "Duplicates"), "Duplicates" -> List("flagstats", "Duplicates"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment") "NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
) )
val results = summary.getStatKeys(runId, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths) val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
val total = results("All").getOrElse(0L).asInstanceOf[Long] val total = results("All").getOrElse(0L).asInstanceOf[Long]
val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long] val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long]
val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long] val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long]
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport) #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File) #import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %> <%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %> <%@ var libId: Option[Int] = None %>
...@@ -84,7 +84,7 @@ ...@@ -84,7 +84,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{ #{
val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
val results = summary.getStatKeys(runId, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths) val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}# }#
#for (field <- fields) #for (field <- fields)
<td>${results(field)}</td> <td>${results(field)}</td>
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport) #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File) #import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %> <%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %> <%@ var libId: Option[Int] = None %>
...@@ -86,7 +86,7 @@ ...@@ -86,7 +86,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{ #{
val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap
val results = summary.getStatKeys(runId, "bammetrics".right, Some("CollectInsertSizeMetrics".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths) val results = summary.getStatKeys(runId, "bammetrics", "CollectInsertSizeMetrics", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}# }#
#for (field <- fields) #for (field <- fields)
<td>${results(field)}</td> <td>${results(field)}</td>
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport) #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File) #import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %> <%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %> <%@ var libId: Option[Int] = None %>
...@@ -85,7 +85,7 @@ ...@@ -85,7 +85,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{ #{
val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
val results = summary.getStatKeys(runId, "bammetrics".right, Some("bamstats".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths) val results = summary.getStatKeys(runId, "bammetrics", "bamstats", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}# }#
#for (field <- fields) #for (field <- fields)
<td>${results(field)}</td> <td>${results(field)}</td>
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport) #import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File) #import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %> <%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %> <%@ var libId: Option[Int] = None %>
...@@ -75,7 +75,7 @@ ...@@ -75,7 +75,7 @@
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{ #{
val statsPaths = fields.map(x => x -> List("metrics", x)).toMap val statsPaths = fields.map(x => x -> List("metrics", x)).toMap
val results = summary.getStatKeys(runId, "bammetrics".right, Some("wgs".right), sample = Some(sample.id.left), library = libId.map(_.left), keyValues = statsPaths) val results = summary.getStatKeys(runId, "bammetrics", "wgs", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths)
}# }#
#for (field <- fields) #for (field <- fields)
<td>${results(field)}</td> <td>${results(field)}</td>
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var rootPath: String %> <%@ var rootPath: String %>
<%@ var pipeline: String %> <%@ var pipeline: String %>
<%@ var runId: Int %> <%@ var runId: Int %>
#{ #{
val settings = summary.getSettingKeys(runId, pipeline,
val settings = summary.getSettingKeys(runId, pipeline.right,
keyValues = Map( keyValues = Map(
"contigs" -> List("reference", "contigs"), "contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"), "species" -> List("reference", "species"),
...@@ -19,7 +17,7 @@ ...@@ -19,7 +17,7 @@
)) ))
val contigs = settings.getOrElse("contigs", Some(Map())).getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]] val contigs = settings.getOrElse("contigs", Some(Map())).getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
val referenceFile = Await.result(summary.getFile(runId, pipeline.right, None, None, None, key = "referenceFasta"), Duration.Inf) val referenceFile = Await.result(summary.getFile(runId, pipeline, key = "referenceFasta"), Duration.Inf)
}# }#
<table class="table"> <table class="table">
......
...@@ -21,13 +21,13 @@ import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Sample } ...@@ -21,13 +21,13 @@ import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Sample }
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand } import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand }
import org.broadinstitute.gatk.utils.commandline.Input import org.broadinstitute.gatk.utils.commandline.Input
import nl.lumc.sasc.biopet.utils.tryToParseNumber
import org.fusesource.scalate.{ TemplateEngine, TemplateSource } import org.fusesource.scalate.{ TemplateEngine, TemplateSource }
import scala.collection.mutable import scala.collection.mutable
import scala.concurrent.{ Await, Future } import scala.concurrent.{ Await, Future }
import scala.concurrent.duration.Duration import scala.concurrent.duration.Duration
import scala.language.postfixOps import scala.language.postfixOps
import scala.language.implicitConversions
/** /**
* This trait is meant to make an extension for a report object * This trait is meant to make an extension for a report object
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport) #import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File) #import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var runId: Int %> <%@ var runId: Int %>
<%@ var sampleId: Option[Int] = None %> <%@ var sampleId: Option[Int] = None %>
...@@ -20,7 +20,7 @@ ...@@ -20,7 +20,7 @@
#{ #{
val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf) val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf) val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val settings = summary.getSettingsForLibraries(runId, "flexiprep".right, keyValues = Map( val settings = summary.getSettingsForLibraries(runId, "flexiprep", keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired"))) "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true)) settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true)) val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
...@@ -28,7 +28,7 @@ ...@@ -28,7 +28,7 @@
val librariesCount = libraries.size val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined) val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true) summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1 else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}# }#
#if (showIntro) #if (showIntro)
...@@ -139,8 +139,8 @@ ...@@ -139,8 +139,8 @@
#if (read == "R2") </tr><tr> #end #if (read == "R2") </tr><tr> #end
#{ #{
val statsPaths = Map("num_total" -> List("bases", "num_total")) val statsPaths = Map("num_total" -> List("bases", "num_total"))
val seqstatStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = statsPaths) val seqstatStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read, sample = sample.id, library = lib.id, keyValues = statsPaths)
val seqstatQcStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = statsPaths) val seqstatQcStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read + "_qc", sample = sample.id, library = lib.id, keyValues = statsPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils) #import(org.apache.commons.io.FileUtils)
#import(java.io.File) #import(java.io.File)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var runId: Int %> <%@ var runId: Int %>
<%@ var sampleId: Option[Int] %> <%@ var sampleId: Option[Int] %>
...@@ -14,7 +14,7 @@ ...@@ -14,7 +14,7 @@
<%@ var plot: String %> <%@ var plot: String %>
<%@ var outputDir: File %> <%@ var outputDir: File %>
#{ #{
val settings = summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map( val settings = summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired"))) "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
val paired: Boolean = settings("paired") == Some(true) val paired: Boolean = settings("paired") == Some(true)
...@@ -22,7 +22,7 @@ ...@@ -22,7 +22,7 @@
val skipTrim: Boolean = settings("skip_trim") == Some(true) val skipTrim: Boolean = settings("skip_trim") == Some(true)
def getPlot(read:String) = { def getPlot(read:String) = {
val file = Await.result(summary.getFile(runId, "flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left), plot), Duration.Inf) val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), plot), Duration.Inf)
file.collect { file.collect {
case path => { case path => {
val file = new File(path.path.toString) val file = new File(path.path.toString)
...@@ -34,7 +34,7 @@ ...@@ -34,7 +34,7 @@
} }
def plotAvailable(read:String) = { def plotAvailable(read:String) = {
val file = Await.result(summary.getFile(runId, "flexiprep".right, Some(read.right), sampleId.map(_.left), libId.map(_.left), plot), Duration.Inf) val file = Await.result(summary.getFile(runId, "flexiprep", read, SampleId(sampleId.get), LibraryId(libId.get), plot), Duration.Inf)
file.map(x => new File(x.path).exists()).getOrElse(false) file.map(x => new File(x.path).exists()).getOrElse(false)
} }
......
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage) #import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await) #import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration) #import(scala.concurrent.duration.Duration)
#import(java.io.File) #import(java.io.File)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport) #import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(scalaz._)
#import(Scalaz._)
<%@ var summary: SummaryDb %> <%@ var summary: SummaryDb %>
<%@ var runId: Int %> <%@ var runId: Int %>
<%@ var sampleId: Option[Int] = None %> <%@ var sampleId: Option[Int] = None %>
...@@ -19,7 +19,7 @@ ...@@ -19,7 +19,7 @@
#{ #{
val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf) val samples = Await.result(summary.getSamples(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf) val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = sampleId), Duration.Inf)
val settings = summary.getSettingsForLibraries(runId, "flexiprep".right, keyValues = Map( val settings = summary.getSettingsForLibraries(runId, "flexiprep", keyValues = Map(
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired"))) "skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true)) settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true)) val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
...@@ -27,7 +27,7 @@ ...@@ -27,7 +27,7 @@
val librariesCount = libraries.size val librariesCount = libraries.size
val paired: Boolean = if (sampleId.isDefined && libId.isDefined) val paired: Boolean = if (sampleId.isDefined && libId.isDefined)
summary.getSettingKeys(runId, "flexiprep".right, None, sampleId.map(_.left), libId.map(_.left), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true) summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1 else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
}# }#
...@@ -144,15 +144,15 @@ ...@@ -144,15 +144,15 @@
#if (read == "R2") </tr><tr> #end #if (read == "R2") </tr><tr> #end
#{ #{
val seqstatPaths = Map("num_total" -> List("reads", "num_total")) val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = seqstatPaths) val seqstatStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read, sample = sample.id, library = lib.id, keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatKeys(runId, "flexiprep".right, Some(("seqstat_" + read + "_qc").right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = seqstatPaths) val seqstatQcStats = summary.getStatKeys(runId, "flexiprep", "seqstat_" + read + "_qc", sample = sample.id, library = lib.id, keyValues = seqstatPaths)
val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"), val clippingPaths = Map("num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long")) "num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val clippingStats = summary.getStatKeys(runId, "flexiprep".right, Some(("clipping_" + read).right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = clippingPaths) val clippingStats = summary.getStatKeys(runId, "flexiprep", "clipping_" + read, sample = sample.id, library = lib.id, keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read)) val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats = summary.getStatKeys(runId, "flexiprep".right, Some("trimming".right), sample = Some(sample.id.left), library = Some(lib.id.left), keyValues = trimmingPaths) val trimmingStats = summary.getStatKeys(runId, "flexiprep", "trimming", sample = sample.id, library = lib.id, keyValues = trimmingPaths)
val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong val beforeTotal = seqstatStats("num_total").getOrElse(0).toString.toLong
val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong val afterTotal = seqstatQcStats("num_total").getOrElse(0).toString.toLong
......
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