From 3427e4e1654497ea7f4a8ef5a97a8c59e06a9895 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 27 Jan 2016 11:55:50 +0100
Subject: [PATCH] Code improvement
---
.../pipelines/mapping/MultisampleMappingReport.scala | 11 ++++-------
1 file changed, 4 insertions(+), 7 deletions(-)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
index 23338c4d1..4207bf0a3 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
@@ -29,8 +29,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
- .filter(_._2.isDefined)
- .nonEmpty
+ .exists { case ((sample, lib), value) => value.isDefined }
ReportPage(
List("Samples" -> generateSamplesPage(pageArgs)) ++
@@ -67,8 +66,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Files page, can be used general or at sample level */
def filesPage: ReportPage = {
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
- .filter(_._2.isDefined)
- .nonEmpty
+ .exists { case ((sample, lib), value) => value.isDefined }
ReportPage(List(), (if (flexiprepExecuted) List(
"Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
@@ -82,9 +80,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
val flexiprepExecuted = summary.getLibraryValues("flexiprep")
- .filter(_._1._1 == sampleId)
- .filter(_._2.isDefined)
- .nonEmpty
+ .exists { case ((sample, lib), value) => sample == sampleId && value.isDefined }
ReportPage(List(
"Libraries" -> generateLibraryPage(args),
@@ -103,6 +99,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Library page */
def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
val flexiprepExecuted = summary.getValue(Some(sampleId), Some(libId), "flexiprep").isDefined
+
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil),
--
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