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Commit ea7282d9 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub
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Merge pull request #24 from biopet/fix-BIOPET-546 

Fix biopet 546
parents 7812d950 8314da08
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Showing with 310 additions and 338 deletions
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/Bam2Wig.scala
View file @ ea7282d9
......@@ -27,7 +27,7 @@ import org.broadinstitute.gatk.queue.QScript
*
* Created by pjvan_thof on 1/29/15.
*/
class Bam2Wig(val root: Configurable) extends QScript with BiopetQScript {
class Bam2Wig(val parent: Configurable) extends QScript with BiopetQScript {
def this() = this(null)
@Input(doc = "Input bam file", required = true)
......
bam2wig/src/main/scala/nl/lumc/sasc/biopet/pipelines/bamtobigwig/BamToChromSizes.scala
View file @ ea7282d9
......@@ -28,7 +28,7 @@ import scala.collection.JavaConversions._
*
* Created by pjvan_thof on 1/29/15.
*/
class BamToChromSizes(val root: Configurable) extends InProcessFunction with Configurable {
class BamToChromSizes(val parent: Configurable) extends InProcessFunction with Configurable {
@Input
var bamFile: File = _
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @ ea7282d9
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
<br/>
......@@ -69,24 +67,31 @@
<th>(%)</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#for (sample <- samples.sortBy(_.name))
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString).sorted
case _ => summary.libraries(sample).toList.sorted
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val total = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val secondary = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
val statsPaths = Map(
"All" -> List("flagstats", "All"),
"Mapped" -> List("flagstats", "Mapped"),
"Duplicates" -> List("flagstats", "Duplicates"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
val total = results("All").getOrElse(0L).asInstanceOf[Long]
val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long]
val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long]
val secondary = results("NotPrimaryAlignment").getOrElse(0L).asInstanceOf[Long]
}#
<td>${total}</td>
<td>${mapped}</td>
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
View file @ ea7282d9
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
......@@ -42,7 +38,7 @@
#end
#if (showPlot)
#{ BammetricsReport.clippingPlot(outputDir, "clipping", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.clippingPlot(outputDir, "clipping", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
<div class="panel-body">
<img src="clipping.png" class="img-responsive" />
......@@ -71,27 +67,25 @@
#end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#for (sample <- samples.sortBy(_.name))
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("bamstats", "clipping", "general", field)):_*).getOrElse("N/A")
}
val statsPaths = fields.map(x => x -> List("clipping", "general", x)).toMap
val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
}#
#for (value <- fieldValues)
<td>${value}</td>
#for (field <- fields)
<td>${results(field)}</td>
#end
</tr>
#end
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @ ea7282d9
......@@ -43,7 +43,7 @@
#end
#if (showPlot)
#{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.insertSizePlot(outputDir, "insertsize", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
<div class="panel-body">
<img src="insertsize.png" class="img-responsive" />
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @ ea7282d9
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
......@@ -42,7 +39,7 @@
#end
#if (showPlot)
#{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
<div class="panel-body">
<img src="mapping_quality.png" class="img-responsive" />
......@@ -71,27 +68,25 @@
#end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#for (sample <- samples.sortBy(_.name))
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("bamstats", "mapping_quality", "general", field)):_*).getOrElse("N/A")
}
val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
}#
#for (value <- fieldValues)
<td>${value}</td>
#for (field <- fields)
<td>${results(field)}</td>
#end
</tr>
#end
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @ ea7282d9
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("mean_coverage", "pct_5x", "pct_10x", "pct_15x", "pct_20x", "pct_25x", "pct_30x", "pct_40x", "pct_50x", "pct_60x", "pct_70x", "pct_80x", "pct_90x", "pct_100x")%>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
......@@ -36,7 +32,7 @@
#end
#if (showPlot)
#{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.wgsHistogramPlot(outputDir, "wgs", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
<div class="panel-body">
<img src="wgs.png" class="img-responsive" />
......@@ -62,27 +58,25 @@
#end
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#for (sample <- samples.sortBy(_.name))
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString)
case _ => summary.libraries(sample).toList
val libs: List[Option[Int]] = (libId, sampleLevel) match {
case (_, true) => List(None)
case (Some(_), _) => List(libId)
case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("wgs", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
}
val statsPaths = fields.map(x => x -> List("metrics", x)).toMap
val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("wgs")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
}#
#for (value <- fieldValues)
<td>${value}</td>
#for (field <- fields)
<td>${results(field)}</td>
#end
</tr>
#end
......
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BamMetrics.scala
View file @ ea7282d9
......@@ -28,7 +28,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.intervals.BedCheck
import org.broadinstitute.gatk.queue.QScript
class BamMetrics(val root: Configurable) extends QScript
class BamMetrics(val parent: Configurable) extends QScript
with SummaryQScript
with SampleLibraryTag
with Reference
......@@ -43,13 +43,6 @@ class BamMetrics(val root: Configurable) extends QScript
override def defaults = Map("bedtoolscoverage" -> Map("sorted" -> true))
/** return location of summary file */
def summaryFile = (sampleId, libId) match {
case (Some(s), Some(l)) => new File(outputDir, s + "-" + l + ".BamMetrics.summary.json")
case (Some(s), _) => new File(outputDir, s + ".BamMetrics.summary.json")
case _ => new File(outputDir, "BamMetrics.summary.json")
}
/** returns files to store in summary */
def summaryFiles = Map("reference" -> referenceFasta(),
"input_bam" -> inputBam) ++
......@@ -63,7 +56,7 @@ class BamMetrics(val root: Configurable) extends QScript
override def reportClass = {
val bammetricsReport = new BammetricsReport(this)
bammetricsReport.outputDir = new File(outputDir, "report")
bammetricsReport.summaryFile = summaryFile
bammetricsReport.summaryDbFile = summaryDbFile
bammetricsReport.args = if (libId.isDefined) Map(
"sampleId" -> sampleId.getOrElse("."),
"libId" -> libId.getOrElse("."))
......
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @ ea7282d9
......@@ -17,11 +17,16 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import java.io.{ File, PrintWriter }
import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportBuilder, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
import nl.lumc.sasc.biopet.utils.rscript.{ StackedBarPlot, LinePlot }
import nl.lumc.sasc.biopet.core.report.{ ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection }
import nl.lumc.sasc.biopet.utils.ConfigUtils
import nl.lumc.sasc.biopet.utils.rscript.{ LinePlot, StackedBarPlot }
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
class BammetricsReport(val root: Configurable) extends ReportBuilderExtension {
import scala.concurrent.ExecutionContext.Implicits.global
import scala.concurrent.Await
import scala.concurrent.duration.Duration
class BammetricsReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = BammetricsReport
}
......@@ -52,23 +57,25 @@ object BammetricsReport extends ReportBuilder {
}
/** Generates a page with alignment stats */
def bamMetricsPage(summary: Summary,
sampleId: Option[String],
libId: Option[String],
def bamMetricsPage(summary: SummaryDb,
sampleId: Option[Int],
libId: Option[Int],
metricsTag: String = "bammetrics") = {
val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
//val pipelineId: Int = summary.getPipelineId(runId, metricsTag).map(_.get)
val insertsizeMetrics = summary.getValue(sampleId, libId, metricsTag, "stats", "CollectInsertSizeMetrics", "metrics") match {
case Some(None) => false
case Some(_) => true
case _ => false
}
val wgsExecuted = summary.getStatsSize(runId, Right(metricsTag), Some(Right("wgs")), sample = sampleId.map(Left(_)), library = libId.map(Left(_))) >= 1
val rnaExecuted = summary.getStatsSize(runId, Right(metricsTag), Some(Right("rna")), sample = sampleId.map(Left(_)), library = libId.map(Left(_))) >= 1
val insertsizeMetrics = summary.getStatKeys(runId, Right(metricsTag), Some(Right("CollectInsertSizeMetrics")),
sample = sampleId.map(Left(_)), library = libId.map(Left(_)), Map("metrics" -> List("metrics")))
.exists(_._2.isDefined)
val targetSettings = summary.getSettingKeys(runId, Right(metricsTag), None, sample = sampleId.map(Left(_)), library = libId.map(Left(_)),
Map("amplicon_name" -> List("amplicon_name"), "roi_name" -> List("roi_name")))
val targets = (
summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
targetSettings("amplicon_name"),
targetSettings("roi_name")
) match {
case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
case (_, Some(roi: List[_])) => roi.map(_.toString)
......@@ -108,44 +115,42 @@ object BammetricsReport extends ReportBuilder {
*/
def alignmentSummaryPlot(outputDir: File,
prefix: String,
summary: Summary,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[String] = None): Unit = {
sampleId: Option[Int] = 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("\tMapped\tDuplicates\tUnmapped\tSecondary")
def getLine(summary: Summary, sample: String, lib: Option[String] = None): String = {
val mapped = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "Mapped"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val duplicates = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "Duplicates"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val total = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "All"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val secondary = new SummaryValue(List("bammetrics", "stats", "bamstats", "flagstats", "NotPrimaryAlignment"),
summary, Some(sample), lib).value.getOrElse(0).toString.toLong
val statsPaths = Map(
"Mapped" -> List("flagstats", "Mapped"),
"Duplicates" -> List("flagstats", "Duplicates"),
"All" -> List("flagstats", "All"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val results: Map[(Int, Option[Int]), Map[String, Option[Any]]] = if (libraryLevel) {
summary.getStatsForLibraries(runId, Right("bammetrics"), Some(Right("bamstats")),
sampleId = sampleId, keyValues = statsPaths).map(x => (x._1._1, Some(x._1._2)) -> x._2)
} else summary.getStatsForSamples(runId, Right("bammetrics"), Some(Right("bamstats")),
sample = sampleId.map(Left(_)), keyValues = statsPaths).map(x => (x._1, None) -> x._2)
for (((s, l), result) <- results) {
val sampleName: String = summary.getSampleName(s).map(_.get)
val libName: Option[String] = l.flatMap(x => Await.result(summary.getLibraryName(x), Duration.Inf))
val sb = new StringBuffer()
if (lib.isDefined) sb.append(sample + "-" + lib.get + "\t") else sb.append(sample + "\t")
if (libName.isDefined) sb.append(sampleName + "-" + libName.get + "\t") else sb.append(sampleName + "\t")
val mapped = ConfigUtils.any2long(result("Mapped"))
val duplicates = ConfigUtils.any2long(result("Duplicates"))
val total = ConfigUtils.any2long(result("All"))
val secondary = ConfigUtils.any2long(result("NotPrimaryAlignment"))
sb.append((mapped - duplicates - secondary) + "\t")
sb.append(duplicates + "\t")
sb.append((total - mapped) + "\t")
sb.append(secondary)
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.println(sb.toString)
}
tsvWriter.close()
......@@ -155,12 +160,56 @@ object BammetricsReport extends ReportBuilder {
plot.output = pngFile
plot.ylabel = Some("Reads")
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))
plot.width = Some(200 + (libraries.filter(s => sampleId.getOrElse(s.id) == s.id).size) * 10)
} else plot.width = Some(200 + (samples.count(s => sampleId.getOrElse(s) == s) * 10))
plot.title = Some("Aligned reads")
plot.runLocal()
}
def writePlotFromSummary(outputDir: File,
prefix: String,
summary: SummaryDb,
libraryLevel: Boolean = false,
sampleId: Option[Int] = None,
libraryId: Option[Int] = None,
statsPaths: Map[String, List[String]],
xKey: String,
yKey: String,
pipeline: Either[Int, String],
module: Option[Either[Int, String]],
xlabel: Option[String] = None,
ylabel: Option[String] = None,
title: Option[String] = None,
removeZero: Boolean = true): Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png")
val results: Map[(Int, Option[Int]), Map[String, Option[Array[Any]]]] = if (libraryLevel) {
summary.getStatsForLibraries(runId, pipeline, module, sampleId = sampleId, keyValues = statsPaths)
.map(x => (x._1._1, Some(x._1._2)) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
} else summary.getStatsForSamples(runId, pipeline, module, sample = sampleId.map(Left(_)), keyValues = statsPaths)
.map(x => (x._1, None) -> x._2.map(x => x._1 -> x._2.map(ConfigUtils.any2list(_).toArray)))
val tables: Array[Map[String, Array[Any]]] = results.map {
case ((sample, library), map) =>
val sampleName = Await.result(summary.getSampleName(sample), Duration.Inf)
.getOrElse(throw new IllegalStateException("Sample must be there"))
val libraryName = library.flatMap(l => Await.result(summary.getLibraryName(l), Duration.Inf))
Map(</