Major release of version 2.3:

- Added container classes to increase abstraction.
- Increased efficiency of computations and memory usage.
- All variant calls are now stored in the build output, including reference. This reduces reference bias by rejecting calls.
- Simplified input parameters (call quality is no longer considered).
- Removed deprecated/redundant and cleaned up code.

build.gradle

@@ -1,7 +1,7 @@
 /*
 Set meta-information for the project build.
 */
-version 'v2.2'
+version 'v2.3'
 group 'de.tue.it'
 
 println "Project: $project"
@@ -84,17 +84,14 @@ dependencies {
     implementation 'org.apache.logging.log4j:log4j-api:2.20.0'
     implementation 'org.biojava:biojava-core:5.4.0'
     implementation 'org.biojava:biojava-genome:5.4.0'
-    implementation 'org.biojava:biojava-structure:5.4.0'
     implementation 'com.github.cliftonlabs:json-simple:4.0.1'
     implementation 'org.javatuples:javatuples:1.2'
     implementation 'com.google.code.gson:gson:2.10.1'
     implementation 'com.google.code.gson:gson-extras:2.8.5'
-    implementation 'net.sourceforge:javaml:0.1.7'
     implementation 'org.apache.commons:commons-text:1.10.0'
     implementation 'com.aayushatharva.brotli4j:brotli4j:1.12.0'
     implementation 'com.aayushatharva.brotli4j:native-windows-x86_64:1.12.0'
     implementation 'com.aayushatharva.brotli4j:native-linux-x86_64:1.12.0'
-    implementation 'org.apache.commons:commons-math3:3.6.1'
     implementation 'com.github.java-json-tools:json-schema-validator:2.2.14'
 }