vcf file created for variants doesn't include nulls

frontend-js/src/main/js/map/data/GeneVariant.js

 "use strict";
 
+/**
+ *
+ * @param {Object} javaObject
+ * @param {number} javaObject.position
+ * @param {string} javaObject.originalDna
+ * @param {string} javaObject.modifiedDna
+ * @param {string} javaObject.referenceGenomeType
+ * @param {string} javaObject.referenceGenomeVersion
+ * @param {string} javaObject.contig
+ * @param {null|number} [javaObject.allelFrequency]
+ * @param {null|string} [javaObject.variantIdentifier]
+ *
+ * @constructor
+ */
 function GeneVariant(javaObject) {
   this.setPosition(javaObject.position);
   this.setOriginalDna(javaObject.originalDna);
@@ -11,68 +25,139 @@ function GeneVariant(javaObject) {
   this.setVariantIdentifier(javaObject.variantIdentifier);
 }
 
-GeneVariant.prototype.setPosition = function(position) {
+/**
+ *
+ * @param {number} position
+ */
+GeneVariant.prototype.setPosition = function (position) {
   this._position = position;
 };
 
-GeneVariant.prototype.getPosition = function() {
+/**
+ *
+ * @returns {number}
+ */
+GeneVariant.prototype.getPosition = function () {
   return this._position;
 };
 
-GeneVariant.prototype.setOriginalDna = function(originalDna) {
+/**
+ *
+ * @param {string} originalDna
+ */
+GeneVariant.prototype.setOriginalDna = function (originalDna) {
   this._original = originalDna;
 };
 
-GeneVariant.prototype.getOriginalDna = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getOriginalDna = function () {
   return this._original;
 };
 
-GeneVariant.prototype.setModifiedDna = function(modifiedDna) {
+/**
+ *
+ * @param {string} modifiedDna
+ */
+GeneVariant.prototype.setModifiedDna = function (modifiedDna) {
   this._modifiedDna = modifiedDna;
 };
 
-GeneVariant.prototype.getModifiedDna = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getModifiedDna = function () {
   return this._modifiedDna;
 };
 
-GeneVariant.prototype.setContig = function(contig) {
+/**
+ *
+ * @param {string} contig
+ */
+GeneVariant.prototype.setContig = function (contig) {
   this._contig = contig;
 };
 
-GeneVariant.prototype.getContig = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getContig = function () {
   return this._contig;
 };
 
-GeneVariant.prototype.setAllelFrequency = function(allelFrequency) {
-  this._allelFrequency = allelFrequency;
+/**
+ *
+ * @param {number} allelFrequency
+ */
+GeneVariant.prototype.setAllelFrequency = function (allelFrequency) {
+  if (allelFrequency === null) {
+    this._allelFrequency = undefined;
+  } else {
+    this._allelFrequency = allelFrequency;
+  }
 };
 
-GeneVariant.prototype.getAllelFrequency = function() {
+/**
+ *
+ * @returns {number}
+ */
+GeneVariant.prototype.getAllelFrequency = function () {
   return this._allelFrequency;
 };
 
-GeneVariant.prototype.setVariantIdentifier = function(variantIdentifier) {
-  this._variantIdentifier = variantIdentifier;
+/**
+ *
+ * @param {string} variantIdentifier
+ */
+GeneVariant.prototype.setVariantIdentifier = function (variantIdentifier) {
+  if (variantIdentifier === null) {
+    this._variantIdentifier = undefined;
+  } else {
+    this._variantIdentifier = variantIdentifier;
+  }
 };
 
-GeneVariant.prototype.getVariantIdentifier = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getVariantIdentifier = function () {
   return this._variantIdentifier;
 };
 
-GeneVariant.prototype.setReferenceGenomeType = function(referenceGenomeType) {
+/**
+ *
+ * @param {string} referenceGenomeType
+ */
+GeneVariant.prototype.setReferenceGenomeType = function (referenceGenomeType) {
   this._referenceGenomeType = referenceGenomeType;
 };
 
-GeneVariant.prototype.getReferenceGenomeType = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getReferenceGenomeType = function () {
   return this._referenceGenomeType;
 };
 
-GeneVariant.prototype.setReferenceGenomeVersion = function(
-    referenceGenomeVersion) {
+/**
+ *
+ * @param {string} referenceGenomeVersion
+ */
+GeneVariant.prototype.setReferenceGenomeVersion = function (referenceGenomeVersion) {
   this._referenceGenomeVersion = referenceGenomeVersion;
 };
 
-GeneVariant.prototype.getReferenceGenomeVersion = function() {
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getReferenceGenomeVersion = function () {
   return this._referenceGenomeVersion;
 };
 

frontend-js/src/main/js/map/window/AliasInfoWindow.js

@@ -355,15 +355,15 @@ AliasInfoWindow.prototype.createGenomicDiv = function () {
       if (genomeUrls.length === 0) {
         contentElement.innerHTML = "No reference genome data available on minerva platform";
       } else {
-        for (var iter = 0; iter < self.layoutAliases.length; iter++) {
-          if (globalGeneVariants[iter].length > 0) {
-            var vcfContent = self.createVcfString(globalGeneVariants[iter]);
+        for (var i= 0; i < self.layoutAliases.length; i++) {
+          if (globalGeneVariants[i].length > 0) {
+            var vcfContent = self.createVcfString(globalGeneVariants[i]);
             pileupSource.push({
               viz: pileup.viz.variants(),
               data: pileup.formats.vcf({
                 content: vcfContent
               }),
-              name: self.layoutNames[iter] + ' - Variants',
+              name: self.layoutNames[i] + ' - Variants',
               options: {
                 variantHeightByFrequency: true
               }

frontend-js/src/test/js/map/window/AliasInfoWindow-test.js

@@ -8,6 +8,7 @@ var functions = require('../../../../main/js/Functions');
 
 var Alias = require('../../../../main/js/map/data/Alias');
 var Drug = require('../../../../main/js/map/data/Drug');
+var GeneVariant = require('../../../../main/js/map/data/GeneVariant');
 var AliasInfoWindow = require('../../../../main/js/map/window/AliasInfoWindow');
 var IdentifiedElement = require('../../../../main/js/map/data/IdentifiedElement');
 var DataOverlay = require('../../../../main/js/map/data/DataOverlay');
@@ -361,4 +362,37 @@ describe('AliasInfoWindow', function () {
     });
   });
 
+  it("createVcfString ", function () {
+    var map = helper.createCustomMap();
+    var alias = helper.createAlias(map);
+    var aliasWindow = new AliasInfoWindow({
+      alias: alias,
+      map: map,
+      marker: helper.createMarker({element: alias, map: map})
+    });
+
+    var nullVal = null;
+
+    var variant = new GeneVariant({
+      contig: "11",
+      modifiedDna: "T",
+      originalDna: "C",
+      position: 233067,
+      referenceGenomeType: "UCSC",
+      referenceGenomeVersion: "hg19",
+      allelFrequency: nullVal,
+      variantIdentifier: nullVal
+    });
+    var variant2 = new GeneVariant({
+      contig: "11",
+      modifiedDna: "T",
+      originalDna: "C",
+      position: 233068,
+      referenceGenomeType: "UCSC",
+      referenceGenomeVersion: "hg19"
+    });
+    var str = aliasWindow.createVcfString([variant, variant2]);
+    assert.ok(str.indexOf("null") === -1,"null shouldn't appear in vcf format");
+  });
+
 });