From e2f5ad5846c9fb171876003c93ff2afe2541bb76 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Sun, 20 Nov 2016 16:08:05 +0100
Subject: [PATCH] Changed reports summary values

---
 .../sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp | 8 ++++----
 .../nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp | 4 ++--
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
index e836fb2fa..8e35b9035 100644
--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
+++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
@@ -83,10 +83,10 @@
                     #if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</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("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
-                        val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
-                        val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
-                        val secondary = summary.getValue((prefixPath ::: List("biopet_flagstat", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
+                        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]
                     }#
                     <td>${total}</td>
                     <td>${mapped}</td>
diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
index aab83e541..f1540198d 100644
--- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
+++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/bamStats.ssp
@@ -12,9 +12,9 @@
 #for (field <- fields)
     <tr><th>${field}</th><td>
     #if (libId.isDefined)
-        ${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "biopet_flagstat", field)}
+        ${summary.getLibraryValue(sampleId.get, libId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
     #else
-        ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "biopet_flagstat", field)}
+        ${summary.getSampleValue(sampleId.get, metricsTag, "stats", "bamstats", "flagstats", field)}
     #end
     </td></tr>
 #end
-- 
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