[GLT-4327] handle full-depth collapsed coverage metric (#247)

oicr-gsi · Dec 19, 2024 · 6cba5ac · 6cba5ac
1 parent 6485299
commit 6cba5ac
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diff --git a/changes/add_fullDepth_collapsedCoverage.md b/changes/add_fullDepth_collapsedCoverage.md
@@ -0,0 +1 @@
+Full-Depth Sequencing Collapsed Coverage metric
diff --git 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
@@ -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);
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		Full-Depth Sequencing Collapsed Coverage metric