Refactoring code to varfish-annotator-core (#68)

This is done in preparation for adding explicit variant caller support.

Closes: #68
Related-Issue: #68
Projected-Results-Impact: none

CHANGES.md

@@ -2,6 +2,7 @@
 
 ## v0.26-SNAPSHOT
 
+- Explicitely model support for SV callers (#68)
 - Removing explicit support for SV2 (#67)
 - Adding end-to-end tests `hg19-chr22` (#61)
 

varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsArgs.java

@@ -104,9 +104,11 @@ public final class AnnotateSvsArgs {
   @Parameter(names = "--write-bnd-mate", description = "Write out BND mates (true, false, or auto)")
   private String writeBndMates = "auto";
 
-  public boolean isHelp() {
-    return help;
-  }
+  @Parameter(
+      names = "skip-filters",
+      description =
+          "Skip records with this filter value (comma-separated list), default is 'LowQual'")
+  private String skipFilters = "LowQual";
 
   public String getRefseqSerPath() {
     return refseqSerPath;
@@ -180,6 +182,10 @@ public String getWriteBndMates() {
     return writeBndMates;
   }
 
+  public String getSkipFilters() {
+    return skipFilters;
+  }
+
   @Override
   public String toString() {
     return "AnnotateSvsArgs{"
@@ -237,6 +243,9 @@ public String toString() {
         + ", writeBndMates=\'"
         + writeBndMates
         + "\'"
+        + ", skipFilters=\'"
+        + skipFilters
+        + "\'"
         + '}';
   }
 }