Bump dependencies, fix warnings, remove dead code (#36)

* chore:bump version 2.1.6 to 2.1.7
chore:bump spring-boot-starter-parent 3.0.5 to 3.1.3
chore:bump jacoco-maven-plugin 0.8.9 to 0.8.10
chore:bump vip-utils 1.2.1 to 1.3.0

* chore:remove dead code

* fix:serialization warnings

pom.xml

@@ -6,13 +6,13 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.0.5</version>
+    <version>3.1.3</version>
     <relativePath/> <!-- lookup parent from repository -->
   </parent>
 
   <groupId>org.molgenis</groupId>
   <artifactId>vip-inheritance-matcher</artifactId>
-  <version>2.1.6</version>
+  <version>2.1.7</version>
 
   <name>vip-inheritance-matcher</name>
   <description>Annotates VCF samples with mendelian violation and possible compound flags and
@@ -44,9 +44,10 @@
   <properties>
     <java.version>17</java.version>
     <commons.cli.version>1.5.0</commons.cli.version>
-    <jacoco-maven-plugin.version>0.8.9</jacoco-maven-plugin.version>
+    <!-- [WARNING] Plugin validation issues were detected, see https://github.com/jacoco/jacoco/issues/1435 -->
+    <jacoco-maven-plugin.version>0.8.10</jacoco-maven-plugin.version>
     <samtools.htsjdk.version>3.0.5</samtools.htsjdk.version>
-    <vip.utils.version>1.2.1</vip.utils.version>
+    <vip.utils.version>1.3.0</vip.utils.version>
   </properties>
 
   <profiles>

src/main/java/org/molgenis/vcf/inheritance/matcher/MissingInfoException.java

@@ -1,8 +1,12 @@
 package org.molgenis.vcf.inheritance.matcher;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class MissingInfoException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
 
   public MissingInfoException(String info) {
     super(format("Input is missing INFO field '%s'.", info));

src/main/java/org/molgenis/vcf/inheritance/matcher/MissingVepAnnotationException.java

@@ -1,9 +1,13 @@
 package org.molgenis.vcf.inheritance.matcher;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class MissingVepAnnotationException extends
     RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
 
   public MissingVepAnnotationException(String field) {
     super(format("VEP annotation is missing field '%s'.", field));