From 6cba5acd421fae5115ce9165c8aaefd0c6b3119e Mon Sep 17 00:00:00 2001
From: Dillan Cooke <dillan.cooke@oicr.on.ca>
Date: Thu, 19 Dec 2024 12:29:10 -0500
Subject: [PATCH] [GLT-4327] handle full-depth collapsed coverage metric (#247)

---
 changes/add_fullDepth_collapsedCoverage.md | 1 +
 pom.xml                                    | 2 +-
 ts/data/sample.ts                          | 3 +++
 3 files changed, 5 insertions(+), 1 deletion(-)
 create mode 100644 changes/add_fullDepth_collapsedCoverage.md

diff --git a/changes/add_fullDepth_collapsedCoverage.md b/changes/add_fullDepth_collapsedCoverage.md
new file mode 100644
index 00000000..44f820e4
--- /dev/null
+++ b/changes/add_fullDepth_collapsedCoverage.md
@@ -0,0 +1 @@
+Full-Depth Sequencing Collapsed Coverage metric
diff --git a/pom.xml b/pom.xml
index 9301cb47..85d183a9 100644
--- a/pom.xml
+++ b/pom.xml
@@ -123,7 +123,7 @@
     <dependency>
       <groupId>ca.on.oicr.gsi.cardea</groupId>
       <artifactId>cardea-data</artifactId>
-      <version>1.18.0</version>
+      <version>1.19.0</version>
     </dependency>
   </dependencies>
 
diff --git a/ts/data/sample.ts b/ts/data/sample.ts
index 75fd7c58..2371cca5 100644
--- a/ts/data/sample.ts
+++ b/ts/data/sample.ts
@@ -93,6 +93,7 @@ export interface Sample extends Qcable {
   mappedToCoding?: number;
   rawCoverage?: number;
   onTargetReads?: number;
+  collapsedCoverage?: number;
   lambdaMethylation?: number;
   lambdaClusters?: number;
   puc19Methylation?: number;
@@ -1169,6 +1170,8 @@ function getMetricValue(metricName: string, sample: Sample): number | null {
       return nullIfUndefined(sample.methylationBeta);
     case "PE Reads":
       return nullIfUndefined(sample.peReads);
+    case "Collapsed Coverage":
+      return nullIfUndefined(sample.collapsedCoverage);
   }
   if (/^Concentration/.test(metricName)) {
     return nullIfUndefined(sample.concentration);