From 2d6d3e79f4170d1807a8db4fa40298ff7f93ed6f Mon Sep 17 00:00:00 2001
From: Ryan Amari <ramari16@gmail.com>
Date: Mon, 26 Feb 2024 10:46:17 -0500
Subject: [PATCH] ALS-5981: Add gene and consequence to variant spec

---
 .../hpds/data/genotype/VariantSpec.java       | 62 +++++++++++++++++--
 .../hpds/etl/genotype/NewVCFLoader.java       | 13 +++-
 2 files changed, 68 insertions(+), 7 deletions(-)

diff --git a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantSpec.java b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantSpec.java
index b244e407..83359789 100644
--- a/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantSpec.java
+++ b/data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantSpec.java
@@ -1,6 +1,7 @@
 package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
 
 import java.io.Serializable;
+import java.util.Objects;
 
 import org.apache.commons.csv.CSVRecord;
 
@@ -13,7 +14,22 @@ public class VariantCoords implements Serializable {
 		public String ref;
 		public String alt;
 		public int qual;
-		public String format;		
+		public String format;
+		public String gene;
+		public String consequence;
+
+		@Override
+		public boolean equals(Object o) {
+			if (this == o) return true;
+			if (o == null || getClass() != o.getClass()) return false;
+			VariantCoords that = (VariantCoords) o;
+			return qual == that.qual && Objects.equals(chromosome, that.chromosome) && Objects.equals(offset, that.offset) && Objects.equals(name, that.name) && Objects.equals(ref, that.ref) && Objects.equals(alt, that.alt) && Objects.equals(format, that.format) && Objects.equals(gene, that.gene) && Objects.equals(consequence, that.consequence);
+		}
+
+		@Override
+		public int hashCode() {
+			return Objects.hash(chromosome, offset, name, ref, alt, qual, format, gene, consequence);
+		}
 	}
 	public static int CHR = 0, OFF = 1, NAME = 2, REF = 3, ALT = 4, QUAL = 5, FILTER = 6, INFO = 7, FORMAT = 8, DATA = 9;
 	public long heteroOffset;
@@ -32,6 +48,20 @@ public VariantSpec(CSVRecord r) {
 		}catch(NumberFormatException e) { 
 			this.metadata.qual  = -1;
 		}
+
+		String[] variantInfo = r.get(INFO).split("[=;]");
+		String gene = "NULL";
+		String consequence = "NULL";
+		for (int i = 0; i < variantInfo.length; i = i + 2) {
+			if ("Gene_with_variant".equals(variantInfo[i])) {
+				gene = variantInfo[i + 1];
+			}
+			if ("Variant_consequence_calculated".equals(variantInfo[i])) {
+				consequence = variantInfo[i + 1];
+			}
+		}
+		this.metadata.gene = gene;
+		this.metadata.consequence = consequence;
 	}
 
 	public VariantSpec(String variant) {
@@ -43,28 +73,48 @@ public VariantSpec(String variant) {
 		this.metadata.ref = segments[2];
 		this.metadata.alt = segments[3];
 		this.metadata.qual = -1;
+		this.metadata.gene = segments[4];
+		this.metadata.consequence = segments[5];
 	}
 
 	public String specNotation() {
 		return this.metadata.chromosome + "," 
 				+ this.metadata.offset + "," + 
-				this.metadata.ref + "," + this.metadata.alt;
+				this.metadata.ref + "," + this.metadata.alt + "," + this.metadata.gene + "," + this.metadata.consequence;
 	}
 
-	@Override
 	public int compareTo(VariantSpec o) {
 		int ret = 0;
 		ret = this.metadata.chromosome.compareTo(o.metadata.chromosome);
-		if(ret == 0) {
+		if (ret == 0) {
 			ret = this.metadata.offset.compareTo(o.metadata.offset);
 		}
-		if(ret == 0) {
+		if (ret == 0) {
 			ret = this.metadata.ref.compareTo(o.metadata.ref);
 		}
-		if(ret == 0) {
+		if (ret == 0) {
 			ret = this.metadata.alt.compareTo(o.metadata.alt);
 		}
+		if (ret == 0) {
+			ret = this.metadata.gene.compareTo(o.metadata.gene);
+		}
+		if (ret == 0) {
+			ret = this.metadata.consequence.compareTo(o.metadata.consequence);
+		}
+
 		return ret;
 	}
 
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		VariantSpec that = (VariantSpec) o;
+		return heteroOffset == that.heteroOffset && homoOffset == that.homoOffset && Objects.equals(metadata, that.metadata);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(heteroOffset, homoOffset, metadata);
+	}
 }
\ No newline at end of file
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java
index 43f6c351..996c4078 100644
--- a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java
+++ b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/NewVCFLoader.java
@@ -470,8 +470,19 @@ private void setMasksForSample(char[][] zygosityMaskStrings, int index, int star
 		}
 
 		private String currentSpecNotation() {
+			String[] variantInfo = currentLineSplit[7].split("[=;]");
+			String gene = "NULL";
+			String consequence = "NULL";
+			for (int i = 0; i < variantInfo.length; i = i + 2) {
+				if ("Gene_with_variant".equals(variantInfo[i])) {
+					gene = variantInfo[i + 1];
+				}
+				if ("Variant_consequence_calculated".equals(variantInfo[i])) {
+					consequence = variantInfo[i + 1];
+				}
+			}
 			return currentLineSplit[0] + "," + currentLineSplit[1] + "," + currentLineSplit[3] + ","
-					+ currentLineSplit[4];
+					+ currentLineSplit[4] + "," + gene + "," + consequence;
 		}
 
 		public void readHeaders(ConcurrentHashMap<String, InfoStore> infoStores) throws IOException {