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