Beacon v0.3 compliance: Length for DEL only

app/node-app/arraymap-beacon/v0.3/beacon-query.js

@@ -63,8 +63,6 @@ function checkPreconditions(params) {
         };
     }
 
-    console.log(Boolean(alternateBasesMap[params.alternateBases]));
-
     if (!params.alternateBases) {
         return {
             hasError: true,
@@ -82,8 +80,11 @@ function checkPreconditions(params) {
 function buildMongoQuery(params) {
 
     var position = parseInt(params.start);
-    // not handled for now...
-    // var length = (params.length.length == 0 ? 0 : parseInt(params.length));
+
+    var length = 0;
+    if(params.alternateBases == 'DEL') {
+        length = (params.length.length == 0 ? 0 : parseInt(params.length));
+    }
 
     var andConditions = [];
     var orConditions  = [];
@@ -104,6 +105,17 @@ function buildMongoQuery(params) {
         var convertedReference = referenceMap[params.assemblyId || defaultReference];
 
         var cond = {};
+        if (length > 0) {
+            cond[convertedReference] = {
+                '$elemMatch': {
+                    'CHRO': params.referenceName,
+                    'SEGTYPE': segType,
+                    'SEGSTOP': position + length, // exact position
+                    'SEGSTART': position // exact position
+                }
+            }
+        }
+        else {
             cond[convertedReference] = {
                 '$elemMatch': {
                     'CHRO': params.referenceName,
@@ -116,6 +128,7 @@ function buildMongoQuery(params) {
                     }
                 }
             }
+        }
         andConditions.push(cond);
         if (orConditions.length > 0) {
             andConditions.push({$or: orConditions});
@@ -159,6 +172,9 @@ function checkResultAndGetResponse(params, samples, countTotal) {
     if (typeof params.length != undefined && params.length != null && params.length != '')
     {
         length = parseInt(params.length);
+        if (params.alternateBases == 'DUP') {
+            responseResource.note = "Length provided but not considered when querying DUP";
+        }
     }
 
     var queryResource = {