[GLT-4327] added sample collapsed coverage field

cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Sample.java

@@ -42,6 +42,7 @@ public class Sample {
   private final String name;
   private final String nucleicAcidType;
   private final BigDecimal onTargetReads;
+  private final BigDecimal collapsedCoverage;
   private final String project;
   private final Integer puc19Clusters;
   private final BigDecimal puc19Methylation;
@@ -104,6 +105,7 @@ private Sample(Builder builder) {
     this.mappedToCoding = builder.mappedToCoding;
     this.rawCoverage = builder.rawCoverage;
     this.onTargetReads = builder.onTargetReads;
+    this.collapsedCoverage = builder.collapsedCoverage;
     this.lambdaMethylation = builder.lambdaMethylation;
     this.lambdaClusters = builder.lambdaClusters;
     this.puc19Methylation = builder.puc19Methylation;
@@ -248,6 +250,10 @@ public BigDecimal getOnTargetReads() {
     return onTargetReads;
   }
 
+  public BigDecimal getCollapsedCoverage() {
+    return collapsedCoverage;
+  }
+
   public String getProject() {
     return project;
   }
@@ -384,6 +390,7 @@ public static class Builder {
     private String name;
     private String nucleicAcidType;
     private BigDecimal onTargetReads;
+    private BigDecimal collapsedCoverage;
     private String project;
     private Integer puc19Clusters;
     private BigDecimal puc19Methylation;
@@ -538,6 +545,11 @@ public Builder onTargetReads(BigDecimal onTargetReads) {
       return this;
     }
 
+    public Builder collapsedCoverage(BigDecimal collapsedCoverage) {
+      this.collapsedCoverage = collapsedCoverage;
+      return this;
+    }
+
     public Builder project(String project) {
       this.project = project;
       return this;

cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java

@@ -433,6 +433,7 @@ protected Map<String, Sample> loadSamples(FileReader fileReader, Map<String, Don
           .mappedToCoding(parseDecimal(json, "mapped_to_coding", false))
           .rawCoverage(parseDecimal(json, "raw_coverage", false))
           .onTargetReads(parseDecimal(json, "on_target_reads", false))
+          .collapsedCoverage(parseDecimal(json, "collapsed_coverage", false))
           .lambdaMethylation(parseDecimal(json, "lambda_methylation", false))
           .lambdaClusters(parseInteger(json, "lambda_clusters", false))
           .puc19Methylation(parseDecimal(json, "puc19_methylation", false))

changes/add_collapsedCoverage.md

@@ -0,0 +1 @@
+Sample collapsed coverage field