From b0c4e7a28e2aef7537bb75dfef76b0be8d0c2b11 Mon Sep 17 00:00:00 2001
From: Dillan Cooke <dillan.cooke@oicr.on.ca>
Date: Fri, 8 Mar 2024 11:32:58 -0500
Subject: [PATCH] [GLT-4101] added new metric fields for cfMeDIPs (#45)

---
 .../ca/on/oicr/gsi/cardea/data/Sample.java    | 36 +++++++++++++++++++
 .../on/oicr/gsi/cardea/server/CaseLoader.java |  3 ++
 changes/add_cfmedips_metrics.md               |  1 +
 3 files changed, 40 insertions(+)
 create mode 100644 changes/add_cfmedips_metrics.md

diff --git a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Sample.java b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Sample.java
index 0d906ec..e95deaa 100644
--- a/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Sample.java
+++ b/cardea-data/src/main/java/ca/on/oicr/gsi/cardea/data/Sample.java
@@ -61,6 +61,9 @@ public class Sample {
   private final String tissueOrigin;
   private final String tissueType;
   private final BigDecimal volume;
+  private final BigDecimal relativeCpgInRegions;
+  private final BigDecimal methylationBeta;
+  private final Integer peReads;
 
   private Sample(Builder builder) {
     this.id = requireNonNull(builder.id);
@@ -101,6 +104,9 @@ private Sample(Builder builder) {
     this.lambdaClusters = builder.lambdaClusters;
     this.puc19Methylation = builder.puc19Methylation;
     this.puc19Clusters = builder.puc19Clusters;
+    this.relativeCpgInRegions = builder.relativeCpgInRegions;
+    this.methylationBeta = builder.methylationBeta;
+    this.peReads = builder.peReads;
     this.qcPassed = builder.qcPassed;
     this.qcReason = builder.qcReason;
     this.qcNote = builder.qcNote;
@@ -316,6 +322,18 @@ public BigDecimal getrRnaContamination() {
     return rRnaContamination;
   }
 
+  public BigDecimal getRelativeCpgInRegions() {
+    return relativeCpgInRegions;
+  }
+
+  public BigDecimal getMethylationBeta() {
+    return methylationBeta;
+  }
+
+  public Integer getPeReads() {
+    return peReads;
+  }
+
   @Override
   public int hashCode() {
     return Objects.hash(id, run, sequencingLane);
@@ -370,6 +388,9 @@ public static class Builder {
     private String tissueOrigin;
     private String tissueType;
     private BigDecimal volume;
+    private BigDecimal relativeCpgInRegions;
+    private BigDecimal methylationBeta;
+    private Integer peReads;
 
     public Sample build() {
       return new Sample(this);
@@ -606,5 +627,20 @@ public Builder volume(BigDecimal volume) {
       return this;
     }
 
+    public Builder relativeCpgInRegions(BigDecimal relativeCpgInRegions) {
+      this.relativeCpgInRegions = relativeCpgInRegions;
+      return this;
+    }
+
+    public Builder methylationBeta(BigDecimal methylationBeta) {
+      this.methylationBeta = methylationBeta;
+      return this;
+    }
+
+    public Builder peReads(Integer peReads) {
+      this.peReads = peReads;
+      return this;
+    }
+
   }
 }
diff --git a/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java b/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java
index 1bcde51..0034f5a 100644
--- a/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java
+++ b/cardea-server/src/main/java/ca/on/oicr/gsi/cardea/server/CaseLoader.java
@@ -397,6 +397,9 @@ protected Map<String, Sample> loadSamples(FileReader fileReader, Map<String, Don
           .lambdaClusters(parseInteger(json, "lambda_clusters", false))
           .puc19Methylation(parseDecimal(json, "puc19_methylation", false))
           .puc19Clusters(parseInteger(json, "puc19_clusters", false))
+          .relativeCpgInRegions(parseDecimal(json, "relative_cpg_in_regions", false))
+          .methylationBeta(parseDecimal(json, "methylation_beta", false))
+          .peReads(parseInteger(json, "pe_reads", false))
           .qcPassed(parseQcPassed(json, "qc_state", true))
           .qcReason(parseString(json, "qc_reason"))
           .qcNote(parseString(json, "qc_note"))
diff --git a/changes/add_cfmedips_metrics.md b/changes/add_cfmedips_metrics.md
new file mode 100644
index 0000000..577f513
--- /dev/null
+++ b/changes/add_cfmedips_metrics.md
@@ -0,0 +1 @@
+New metrics for cfMeDIPs assays