chore:bump dependencies, resolve warnings

pom.xml

@@ -7,13 +7,13 @@
   <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-decision-tree</artifactId>
-  <version>3.7.0</version>
+  <version>3.7.1</version>
 
   <name>vip-decision-tree</name>
   <description>Decision tree module for filtering and labelling VCF files</description>
@@ -41,9 +41,9 @@
   <properties>
     <java.version>17</java.version>
     <commons.cli.version>1.5.0</commons.cli.version>
-    <samtools.htsjdk.version>3.0.5</samtools.htsjdk.version>
-    <jacoco-maven-plugin.version>0.8.9</jacoco-maven-plugin.version>
-    <vip.utils.version>1.4.0</vip.utils.version>
+    <samtools.htsjdk.version>4.0.1</samtools.htsjdk.version>
+    <jacoco-maven-plugin.version>0.8.10</jacoco-maven-plugin.version>
+    <vip.utils.version>1.4.1</vip.utils.version>
   </properties>
 
   <profiles>

src/main/java/org/molgenis/vcf/decisiontree/filter/Allele.java

@@ -11,5 +11,5 @@
 public class Allele {
 
   @NonNull String bases;
-  @NonNull int index;
+  int index;
 }

src/main/java/org/molgenis/vcf/decisiontree/filter/EvaluationException.java

@@ -4,8 +4,11 @@
 
 import org.molgenis.vcf.decisiontree.filter.model.Node;
 
-public class EvaluationException extends RuntimeException {
+import java.io.Serial;
 
+public class EvaluationException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public EvaluationException(Node node, Variant variant, String message) {
     super(
         format(

src/main/java/org/molgenis/vcf/decisiontree/filter/FlagListException.java

@@ -1,9 +1,12 @@
 package org.molgenis.vcf.decisiontree.filter;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class FlagListException extends RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "INFO field '%s' of type FLAG cannot contain a list of values.";
   private final String field;
 

src/main/java/org/molgenis/vcf/decisiontree/filter/InvalidNumberOfTokensException.java

@@ -2,11 +2,13 @@
 
 import static java.lang.String.format;
 
+import java.io.Serial;
 import java.util.List;
 import org.molgenis.vcf.decisiontree.filter.model.FieldType;
 
 public class InvalidNumberOfTokensException extends RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "Unsupported number of tokens for input '%s' expecting %d tokens for fieldtype '%s'.";
   private final List<String> fieldTokens;
   private final FieldType type;

src/main/java/org/molgenis/vcf/decisiontree/filter/MissingPhenotypesException.java

@@ -1,10 +1,13 @@
 package org.molgenis.vcf.decisiontree.filter;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class MissingPhenotypesException extends
     RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "Attempting to filter on phenotypes without specifying phenotypes for smaple '%s'.";
   private final String sample;
 

src/main/java/org/molgenis/vcf/decisiontree/filter/UnknownFieldException.java

@@ -5,9 +5,12 @@
 
 import org.molgenis.vcf.decisiontree.filter.model.FieldType;
 
+import java.io.Serial;
+
 public class UnknownFieldException extends
     RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "Unknown '%s' field '%s'.";
   private final String field;
   private final FieldType type;

src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFieldException.java

@@ -1,10 +1,13 @@
 package org.molgenis.vcf.decisiontree.filter;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class UnsupportedFieldException extends
     RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "Unsupported field '%s'.";
   private final String rootField;
 

src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedFormatFieldException.java

@@ -1,10 +1,13 @@
 package org.molgenis.vcf.decisiontree.filter;
 
+import java.io.Serial;
+
 import static java.util.Objects.requireNonNull;
 
 public class UnsupportedFormatFieldException extends
     RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private final Class<?> clazz;
 
   public UnsupportedFormatFieldException(Class<?> clazz) {

src/main/java/org/molgenis/vcf/decisiontree/filter/UnsupportedNestedFieldException.java

@@ -1,8 +1,11 @@
 package org.molgenis.vcf.decisiontree.filter;
 
+import java.io.Serial;
+
 public class UnsupportedNestedFieldException extends
     RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   private final String field;
 
   public UnsupportedNestedFieldException(String field) {

src/main/java/org/molgenis/vcf/decisiontree/filter/model/NestedField.java

@@ -11,7 +11,6 @@
 @NonFinal
 public class NestedField extends FieldImpl implements Comparable<NestedField> {
 
-  @NonNull
   final int index;
   @NonNull
   final Field parent;

src/main/java/org/molgenis/vcf/decisiontree/loader/ConfigDecisionTreeValidationException.java

@@ -1,7 +1,10 @@
 package org.molgenis.vcf.decisiontree.loader;
 
-public class ConfigDecisionTreeValidationException extends RuntimeException {
+import java.io.Serial;
 
+public class ConfigDecisionTreeValidationException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public ConfigDecisionTreeValidationException(String message) {
     super(message);
   }

src/main/java/org/molgenis/vcf/decisiontree/runner/CountMismatchException.java

@@ -4,10 +4,13 @@
 
 import org.molgenis.vcf.decisiontree.loader.model.ConfigBoolQuery;
 
-public class CountMismatchException extends RuntimeException {
+import java.io.Serial;
 
+public class CountMismatchException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public CountMismatchException(ConfigBoolQuery query) {
     super(
-        format("Query value for field '%s' should be a collection for query '%s'.", query.getField(), query.toString()));
+        format("Query value for field '%s' should be a collection for query '%s'.", query.getField(), query));
   }
 }

src/main/java/org/molgenis/vcf/decisiontree/runner/FileValueNotAllowedException.java

@@ -4,8 +4,11 @@
 
 import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator;
 
-public class FileValueNotAllowedException extends RuntimeException {
+import java.io.Serial;
 
+public class FileValueNotAllowedException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public FileValueNotAllowedException(ConfigOperator operator, String allowedFileOperators,
       String field) {
     super(

src/main/java/org/molgenis/vcf/decisiontree/runner/MissingProbandsException.java

@@ -2,10 +2,12 @@
 
 import static java.lang.String.format;
 
+import java.io.Serial;
 import java.util.List;
 
 public class MissingProbandsException extends RuntimeException {
-
+    @Serial
+    private static final long serialVersionUID = 1L;
   public MissingProbandsException(List<String> probands) {
     super(
         format(

src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedOperatorException.java

@@ -6,8 +6,11 @@
 import org.molgenis.vcf.decisiontree.filter.model.Field;
 import org.molgenis.vcf.decisiontree.loader.model.ConfigOperator;
 
-public class UnsupportedOperatorException extends RuntimeException {
+import java.io.Serial;
 
+public class UnsupportedOperatorException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public UnsupportedOperatorException(ConfigOperator operator, Field field,
       DecisionType decisionType) {
     super(

src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountException.java

@@ -5,8 +5,11 @@
 import org.molgenis.vcf.decisiontree.filter.model.DecisionType;
 import org.molgenis.vcf.decisiontree.filter.model.Field;
 
-public class UnsupportedValueCountException extends RuntimeException {
+import java.io.Serial;
 
+public class UnsupportedValueCountException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public UnsupportedValueCountException(Field field, DecisionType decisionType) {
     super(
         format(

src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueCountTypeException.java

@@ -5,8 +5,11 @@
 import org.molgenis.vcf.decisiontree.filter.model.DecisionType;
 import org.molgenis.vcf.decisiontree.filter.model.Field;
 
-public class UnsupportedValueCountTypeException extends RuntimeException {
+import java.io.Serial;
 
+public class UnsupportedValueCountTypeException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public UnsupportedValueCountTypeException(Field field, DecisionType decisionType) {
     super(
         format(

src/main/java/org/molgenis/vcf/decisiontree/runner/UnsupportedValueTypeException.java

@@ -5,8 +5,11 @@
 import org.molgenis.vcf.decisiontree.filter.model.DecisionType;
 import org.molgenis.vcf.decisiontree.filter.model.Field;
 
-public class UnsupportedValueTypeException extends RuntimeException {
+import java.io.Serial;
 
+public class UnsupportedValueTypeException extends RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   public UnsupportedValueTypeException(Field field, DecisionType decisionType) {
     super(
         format(

src/main/java/org/molgenis/vcf/decisiontree/runner/info/InvalidHeaderLineException.java

@@ -1,9 +1,13 @@
 package org.molgenis.vcf.decisiontree.runner.info;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class InvalidHeaderLineException extends
     RuntimeException {
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "VCF header with id '%s' is not a SnpEff header.";
 
   public InvalidHeaderLineException(String id) {

src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingRequiredNestedValueException.java

@@ -1,8 +1,12 @@
 package org.molgenis.vcf.decisiontree.runner.info;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class MissingRequiredNestedValueException extends RuntimeException{
+  @Serial
+  private static final long serialVersionUID = 1L;
   private static final String MESSAGE = "For '%s' annotations the '%s' field is expected to be present.";
 
   public MissingRequiredNestedValueException(String fieldName, String nestedFieldName) {

src/main/java/org/molgenis/vcf/decisiontree/runner/info/MissingVepException.java

@@ -1,8 +1,11 @@
 package org.molgenis.vcf.decisiontree.runner.info;
 
+import java.io.Serial;
+
 public class MissingVepException extends
     RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   @Override
   public String getMessage() {
     return "Input VCF is missing required VEP annotation.";

src/main/java/org/molgenis/vcf/decisiontree/utils/TypeConversionException.java

@@ -1,9 +1,12 @@
 package org.molgenis.vcf.decisiontree.utils;
 
+import java.io.Serial;
+
 import static java.lang.String.format;
 
 public class TypeConversionException extends RuntimeException {
-
+  @Serial
+  private static final long serialVersionUID = 1L;
   public TypeConversionException(Object value, Class<?> thatClass) {
     super(
         format(