Fix VariantMask serialization bug

data/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasks.java

@@ -2,11 +2,13 @@
 
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import com.fasterxml.jackson.databind.annotation.JsonSerialize;
 import com.fasterxml.jackson.databind.ser.std.ToStringSerializer;
 
 import java.io.Serializable;
 import java.math.BigInteger;
+import java.util.Objects;
 
 public class VariantMasks implements Serializable {
 	private static final long serialVersionUID = 6225420483804601477L;
@@ -174,20 +176,73 @@ public VariantMasks(char[][] maskValues) {
 	public VariantMasks() {
 	}
 
+
+	public BigInteger homozygousMask;
+
+	public BigInteger heterozygousMask;
+
+	public BigInteger homozygousNoCallMask;
+
+	public BigInteger heterozygousNoCallMask;
+
+
 	@JsonProperty("ho")
 	@JsonInclude(JsonInclude.Include.NON_NULL)
 	@JsonSerialize(using = ToStringSerializer.class)
-	public BigInteger homozygousMask;
+	public BigInteger getHomozygousMask() {
+		return homozygousMask;
+	}
+
+	@JsonProperty("ho")
+	public void setHomozygousMask(String homozygousMask) {
+		this.homozygousMask = new BigInteger(homozygousMask);
+	}
+
 	@JsonProperty("he")
 	@JsonSerialize(using = ToStringSerializer.class)
 	@JsonInclude(JsonInclude.Include.NON_NULL)
-	public BigInteger heterozygousMask;
+	public BigInteger getHeterozygousMask() {
+		return heterozygousMask;
+	}
+	@JsonProperty("he")
+	public void setHeterozygousMask(String heterozygousMask) {
+		this.heterozygousMask = new BigInteger(heterozygousMask);
+	}
+
 	@JsonProperty("hon")
 	@JsonSerialize(using = ToStringSerializer.class)
 	@JsonInclude(JsonInclude.Include.NON_NULL)
-	public BigInteger homozygousNoCallMask;
+	public BigInteger getHomozygousNoCallMask() {
+		return homozygousNoCallMask;
+	}
+
+	@JsonProperty("hon")
+	public void setHomozygousNoCallMask(String homozygousNoCallMask) {
+		this.homozygousNoCallMask = new BigInteger(homozygousNoCallMask);
+	}
+
 	@JsonProperty("hen")
 	@JsonSerialize(using = ToStringSerializer.class)
 	@JsonInclude(JsonInclude.Include.NON_NULL)
-	public BigInteger heterozygousNoCallMask;
+	public BigInteger getHeterozygousNoCallMask() {
+		return heterozygousNoCallMask;
+	}
+	@JsonProperty("hen")
+	public void setHeterozygousNoCallMask(String heterozygousNoCallMask) {
+		this.heterozygousNoCallMask = new BigInteger(heterozygousNoCallMask);
+	}
+
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		VariantMasks that = (VariantMasks) o;
+		return Objects.equals(homozygousMask, that.homozygousMask) && Objects.equals(heterozygousMask, that.heterozygousMask) && Objects.equals(homozygousNoCallMask, that.homozygousNoCallMask) && Objects.equals(heterozygousNoCallMask, that.heterozygousNoCallMask);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(homozygousMask, heterozygousMask, homozygousNoCallMask, heterozygousNoCallMask);
+	}
 }

data/src/test/java/edu/harvard/hms/dbmi/avillach/hpds/data/genotype/VariantMasksSerializationTest.java

@@ -0,0 +1,48 @@
+package edu.harvard.hms.dbmi.avillach.hpds.data.genotype;
+
+import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.junit.jupiter.api.Test;
+
+import java.math.BigInteger;
+import java.util.concurrent.ThreadLocalRandom;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+public class VariantMasksSerializationTest {
+
+    @Test
+    public void testFieldMaxLength() throws JsonProcessingException {
+        VariantMasks variantMasks = new VariantMasks();
+
+        StringBuilder homozygousStr = new StringBuilder();
+        for (int i = 0 ; i < 5000; i++) {
+            homozygousStr.append(ThreadLocalRandom.current().nextInt(0, 10));
+        }
+        variantMasks.homozygousMask = new BigInteger(homozygousStr.toString());
+
+        StringBuilder heterozygousStr = new StringBuilder();
+        for (int i = 0 ; i < 5000; i++) {
+            heterozygousStr.append(ThreadLocalRandom.current().nextInt(0, 10));
+        }
+        variantMasks.heterozygousMask = new BigInteger(heterozygousStr.toString());
+
+        StringBuilder homozygousNoCallStr = new StringBuilder();
+        for (int i = 0 ; i < 5000; i++) {
+            homozygousNoCallStr.append(ThreadLocalRandom.current().nextInt(0, 10));
+        }
+        variantMasks.homozygousNoCallMask = new BigInteger(homozygousNoCallStr.toString());
+
+        StringBuilder heterozygousNoCallStr = new StringBuilder();
+        for (int i = 0 ; i < 5000; i++) {
+            heterozygousNoCallStr.append(ThreadLocalRandom.current().nextInt(0, 10));
+        }
+        variantMasks.heterozygousNoCallMask = new BigInteger(heterozygousNoCallStr.toString());
+
+        ObjectMapper objectMapper = new ObjectMapper();
+        String serialized = objectMapper.writeValueAsString(variantMasks);
+        VariantMasks deserialized = objectMapper.readValue(serialized, VariantMasks.class);
+
+        assertEquals(variantMasks, deserialized);
+    }
+}