Fixed an issue with sample grouping; Grouping samples now ignores rej…

…ected variants completely.

src/main/java/cli/CLIParser.java

@@ -316,12 +316,6 @@ private void addExportTableOptions(Options options) {
                         .hasArg()
                         .build()
         );
-        options.addOption(
-                Option.builder("x")
-                        .longOpt("rejected")
-                        .desc("Whether to write rejected variants as reference content (Default: Rejected as ambiguous base). This option is only relevant for `content=nucleotide`.")
-                        .build()
-        );
         options.addOption(
                 Option.builder("g")
                         .longOpt("group")

src/main/java/datastructure/VariantAnnotation.java

@@ -1,7 +1,9 @@
 package datastructure;
 
+import main.Musial;
 import main.MusialConstants;
 
+import java.util.ArrayList;
 import java.util.NavigableSet;
 import java.util.concurrent.ConcurrentSkipListMap;
 
@@ -90,5 +92,18 @@ public boolean hasProperty(String key) {
         return this.properties.containsKey(key);
     }
 
+    /**
+     * Returns a list of sample names in which this variant occurs.
+     *
+     * @return {@link ArrayList} of sample names that yield this variant.
+     */
+    public ArrayList<String> getSamples() {
+        ArrayList<String> sampleNames = new ArrayList<>();
+        for (String propertyKey : this.getPropertyKeys()) {
+            if ( propertyKey.startsWith(MusialConstants.VARIANT_OCCURRENCE_SAMPLE_PREFIX) )
+                sampleNames.add( propertyKey.replace( MusialConstants.VARIANT_OCCURRENCE_SAMPLE_PREFIX, "" ) );
+        }
+        return sampleNames;
+    }
 
 }