Add support for ExcessHet

Author: bbimber

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

@@ -49,6 +49,9 @@ public Provider()
                     }}, null),
                     ToolParameterDescriptor.create("impact", "IMPACT", "If selected, the Impact annotation will run, which parses the SnpEff ANN field into multiple discrete INFO fields.", "checkbox", new JSONObject(){{
                         put("checked", false);
+                    }}, null),
+                    ToolParameterDescriptor.create("excessHet", "ExcessHet", "If selected, the ExcessHet annotation will run.", "checkbox", new JSONObject(){{
+                        put("checked", false);
                     }}, null)
             ), null, "");
         }
@@ -106,6 +109,12 @@ public Output processVariants(File inputVCF, File outputDirectory, ReferenceGeno
             options.add("Impact");
         }
 
+        if (getProvider().getParameterByName("excessHet").extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), Boolean.class, false))
+        {
+            options.add("-A");
+            options.add("ExcessHet");
+        }
+
         if (intervals != null)
         {
             intervals.forEach(interval -> {