From f6ea9831d94d20c33918a6358d738750e5f8e0a2 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Fri, 24 Feb 2017 15:10:19 +0100
Subject: [PATCH] Fixed rowspans in flexiprep

---
 .../biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp    | 5 ++---
 .../biopet/pipelines/flexiprep/flexiprepReadSummary.ssp    | 7 +++----
 2 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp b/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
index f4d5c9190..52cca9179 100644
--- a/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
+++ b/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
@@ -112,8 +112,8 @@
         #for (sample <- samples.sortBy(_.name))
             #{
                 val sampleRowspan = {
-                libraries.size +
-                settings.count(_._2("paired").getOrElse(false) == true)
+                libraries.filter(_.sampleId == sample.id).size +
+                settings.filter(_._1._1 == sample.id).count(_._2("paired").getOrElse(false) == true)
                 }
             }#
             <tr><td rowspan="${sampleRowspan}">
@@ -124,7 +124,6 @@
             #end
             </td>
             #for (lib <- libraries.filter(_.sampleId == sample.id))
-                #if (Some(lib.id) != libId) <tr> #end
                     #{ val paired = settings.filter(_._1._1 == sample.id).filter(_._1._2 == lib.id).head._2("paired") == Some(true) }#
                     <td #if (paired == true) rowspan="2" #end>
                     #if (multisample)
diff --git a/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp b/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
index 6741cb45d..b24fc9826 100644
--- a/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
+++ b/flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
@@ -117,8 +117,8 @@
         #for (sample <- samples.sortBy(_.name))
             #{
                 val sampleRowspan = {
-                libraries.size +
-                 settings.count(_._2("paired").getOrElse(false) == true)
+                libraries.filter(_.sampleId == sample.id).size +
+                 settings.filter(_._1._1 == sample.id).count(_._2("paired").getOrElse(false) == true)
                 }
             }#
             <tr><td rowspan="${sampleRowspan}">
@@ -129,13 +129,12 @@
             #end
             </td>
             #for (lib <- libraries.filter(_.sampleId == sample.id))
-                #if (Some(libraries.head.id) != libId) <tr> #end
                     #{ val paired = settings.filter(_._1._1 == sample.id).filter(_._1._2 == lib.id).head._2("paired") == Some(true) }#
                     <td #if (paired == true) rowspan="2" #end>
                     #if (multisample)
                         <a href="${rootPath}Samples/${sample.name}/Libraries/${lib.name}/index.html">${lib.name}</a>
                     #else
-                        ${libId}
+                        ${lib.name}
                     #end
                     </td>
                     #{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
-- 
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