Support ChromosomeCounts annotation

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/variant/VariantAnnotatorStep.java

@@ -43,6 +43,9 @@ public Provider()
                     }}, null),
                     ToolParameterDescriptor.create("maf", "Minor Allele Frequency", "If selected, MAF will be annotated.", "checkbox", new JSONObject(){{
                         put("checked", true);
+                    }}, null),
+                    ToolParameterDescriptor.create("chromosomeCounts", "Chromosome Counts", "If selected, GATK ChromosomeCounts annotations, including AF and AC, will be annotated.", "checkbox", new JSONObject(){{
+                        put("checked", false);
                     }}, null)
             ), null, "");
         }
@@ -87,6 +90,12 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             options.add("MinorAlleleFrequency");
         }
 
+        if (getProvider().getParameterByName("chromosomeCounts").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false))
+        {
+            options.add("-A");
+            options.add("ChromosomeCounts");
+        }
+
         if (intervals != null)
         {
             intervals.forEach(interval -> {