Merge pull request #1122 from iobio/gene_4.11

Gene 4.11.3 merged to master

Author: tonydisera

client/app/components/pages/GeneHome.vue

@@ -69,6 +69,7 @@
       padding-right: 0px
       max-width: 280px
       overflow-wrap: break-word
+      line-height: 20px
 
     &.success--text
       div

client/app/components/partials/AlertPanel.vue

@@ -10,7 +10,8 @@
   padding-right: 20px
 
     
-  #invalid-build-alert    
+  #invalid-build-alert,
+  #invalid-file-combo-alert  
     margin-left: 40px
     padding: 5px
     min-width: 510px
@@ -160,18 +161,23 @@
 
             <v-layout row nowrap class="mt-0">
              <v-card-title class="headline">Files</v-card-title>
+               <div style="display:flex; flex-direction:column">
+                <v-alert id="invalid-file-combo-alert" v-if="!isValidFileCombo"  :value="true" color="error" icon="warning" outline>
+                    Invalid file combination for trio. If one of the trio samples loads alignments but not a variant file, the other samples must follow the same pattern, loading the alignment files only.
+                  </v-alert>
 
-               <v-alert id="invalid-build-alert" v-if="!isValidBuild"  :value="true" color="error" icon="warning" outline>
-                  {{ invalidBuildMessage}}
+                <v-alert id="invalid-build-alert" v-if="!isValidBuild"  :value="true" color="error" icon="warning" outline>
+                    {{ invalidBuildMessage}}
                 </v-alert>
+              </div>
               <v-flex xs12 class="mt-2 text-xs-right">
                 <div class="loader" v-show="inProgress">
                   <img src="../../../assets/images/wheel.gif">
                 </div>
 
                 <v-btn class="load-button action-button"
                   @click="onLoad"
-                  :disabled="!isValid || !buildName">
+                  :disabled="!isValid || !buildName || !isValidFileCombo">
                   Load
                 </v-btn>
 
@@ -331,6 +337,7 @@ export default {
     return {
       showFilesDialog: false,
       isValid: false,
+      isValidFileCombo: true,
       isValidBuild: true,
       invalidBuildMessage: '',
       areAnyDuplicates: false,
@@ -680,6 +687,7 @@ export default {
       })
     },
     validate: function() {
+      this.isValidFileCombo = false;
       this.isValid = false;
       this.cohortModel.isLoaded = false;
       if (this.mode == 'single') {
@@ -691,10 +699,16 @@ export default {
         if (this.modelInfoMap.proband && this.modelInfoMap.proband.model && this.modelInfoMap.proband.model.isReadyToLoad()
             && this.modelInfoMap.mother && this.modelInfoMap.mother.model && this.modelInfoMap.mother.model.isReadyToLoad()
             && this.modelInfoMap.father && this.modelInfoMap.father.model && this.modelInfoMap.father.model.isReadyToLoad()) {
-          this.isValid = true;
-          this.cohortModel.isLoaded = true;
+
+            this.isValid = true;
+            this.cohortModel.isLoaded = true;            
+        
         }
       }
+      if (this.cohortModel.isValidAlignmentsOnly()) {
+        this.isValidFileCombo = true;
+      } 
+
       if (this.isValid && this.cohortModel.isLoaded) {
         this._validateBuild();
       }

client/app/components/partials/FilesDialog.vue

@@ -186,7 +186,7 @@ a {
               <phenotype-search
               v-if="isEduMode"
               :isNav="false"
-              :defaultTopGenes="isEduMode ? '6' : '30'"
+              :defaultTopGenes="isEduMode ? '10' : '30'"
               :phenotypeLabel="isEduMode ? 'Disorder' : 'Phenotype'"
               :geneModel="geneModel"
               :phenotypeLookupUrl="phenotypeLookupUrl"
@@ -391,23 +391,24 @@ export default {
     promiseValidateGene: function(geneName) {
       let self = this;
       return new Promise(function(resolve, reject) {
-        let theGeneName = geneName.toUpperCase();
-        let lookupObject = self.validGenesMap[theGeneName]
+        let theGeneName = geneName;
+        let theGeneNameUC = geneName.toUpperCase();
+        let lookupObject = self.validGenesMap[theGeneNameUC]
         if (lookupObject) {
           resolve(lookupObject)
         } else {
-          self.geneModel.promiseLookupGene(theGeneName)
+          self.geneModel.promiseGetValidGeneName(theGeneName, false)
           .then(function(lookupObject) {
             let match = null;
-            if (lookupObject && typeof(lookupObject) == 'string' && lookupObject.toUpperCase() == theGeneName) {
+            if (lookupObject && typeof(lookupObject) == 'string' && lookupObject.toUpperCase() == theGeneNameUC) {
               match = lookupObject;
-              self.validGenesMap[theGeneName] = theGeneName;
-            } else if (lookupObject && lookupObject.hasOwnProperty('gene_alias') && lookupObject.gene_alias.toUpperCase() == theGeneName) {
+              self.validGenesMap[theGeneNameUC] = lookupObject;
+            } else if (lookupObject && lookupObject.hasOwnProperty('gene_alias') && lookupObject.gene_alias.toUpperCase() == theGeneNameUC) {
               match = lookupObject;
-              self.validGenesMap[theGeneName] = lookupObject;
+              self.validGenesMap[theGeneNameUC] = lookupObject;
             }
             if (match == null) {
-              self.validGenesMap[theGeneName] = false;
+              self.validGenesMap[theGeneNameUC] = false;
             }
             resolve(match)
           })
@@ -441,6 +442,8 @@ export default {
         let lookupObject = self.validGenesMap[geneName.toUpperCase()];
         if (lookupObject && lookupObject.hasOwnProperty('gene_alias')) {
           theGeneName = lookupObject['gene_name']
+        } else if (lookupObject && typeof(lookupObject) == "string") {
+          theGeneName = lookupObject
         }
         return theGeneName;
       }).join(", ")
@@ -498,7 +501,6 @@ export default {
           return gene.geneName;
         })
         .join(", ");
-
       }
     },
     onClearAllGenes: function() {

client/app/components/partials/GenesMenu.vue

@@ -167,8 +167,8 @@ export default {
       },
       formatCircleText: {
         type: Function,
-        default: function(pos, depth) {
-          return depth + 'x' ;
+        default: function(pos, depth, depthSource) {
+          return  + depth + (depthSource && depthSource == "average_base_coverage" ? "x" : " reads");
         }
       }
 
@@ -242,7 +242,7 @@ export default {
         this.$emit('updateDepthChart', this.depthChart);
       },
       showCurrentPoint: function(point) {
-        this.depthChart.showCircle()(point.pos, point.depth, point.altCount);
+        this.depthChart.showCircle()(point.pos, point.depth, point.altCount, point.depthSource);
       },
       hideCurrentPoint: function(point) {
         this.depthChart.hideCircle()();

client/app/components/viz/DepthViz.vue

@@ -310,7 +310,7 @@
             promisePopulateAliases: function() {
               let self = this;
               self.aliases = ""
-              self.cohortModel.geneModel.promiseGetKnownGene(self.selectedGene.gene_name)
+              self.cohortModel.geneModel.promiseGetGeneEntry(self.selectedGene.gene_name)
               .then(function(knownGeneEntry) {
                 if (knownGeneEntry && knownGeneEntry.aliases && knownGeneEntry.aliases.length > 0) {
                   // Add a space after the comma for word wrapping

client/app/components/viz/GeneVariantsCard.vue

@@ -361,6 +361,16 @@ nav.toolbar, nav.v-toolbar
       padding: 0px 5px
       font-size: 11px
       font-weight: 500
+      
+  #project-badge
+    margin-left: -20px
+    .v-chip__content
+      max-width: 120px
+      white-space: normal
+      line-height: 11px
+      padding: 5px 5px 5px 5px
+      text-align: center
+      height: min-content
 
   .toolbar__content
     margin-top: 2px
@@ -797,6 +807,11 @@ nav.toolbar, nav.v-toolbar
         v-tooltip.bottom-left="{content: 'Patient phenotypes'}">
           <v-icon style="font-size: 26px;padding-top: 3px;">account_box</v-icon>
       </v-btn>
+      <v-chip v-if="cohortModel && launchedFromHub && cohortModel.isLoaded && project && project.name"
+          id="project-badge" class="settings-badge" text-color="white">
+          {{ project.name }}
+      </v-chip>
+
 
       <v-btn  class="navbar-icon-button" v-if="appAlerts" id="notification-button"  @click="onShowNotificationDrawer" flat
         v-tooltip.bottom-left="{content: 'Notifications (errors, warnings and information). Click to see detailed list.'}">
@@ -1259,18 +1274,21 @@ nav.toolbar, nav.v-toolbar
               <div id="versions" >
                 <div><span class="version-label">Human Genome Reference</span><span class="number">GRCh37, GRCh38</span></div>
                 <div><span class="version-label">Gencode Human Reference</span><span class="number">19, 25</span></div>
+                
                 <div><span class="version-label">REFSEQ Human Reference</span><span class="number">ref_GRCh37.p5, ref_GRCh38.p7</span></div>
                 <div><span class="version-label">Human Phenotype Ontology</span><span class="number">Build #102 (12-15-2015)</span></div>
-                <div><div class="version-label">Phenolyzer</div><div class="number">Oct 2019</div></div>
+                <div><div class="version-label">gnomAD</div><div class="number">v2.1 for GRCh37, v4 for GRCh38 </div></div>
+                <div><div class="version-label">ACMG Genes</div> <div class="number">v3.2</div></div>
+                <div><span class="version-label">phyloP</span><span class="number">phyloP100way</span></div>
+                
                 <div><div class="version-label">Variant Effect Predictor</div><div class="number">Version 105</div></div>
+                <div><div class="version-label">Phenolyzer</div><div class="number">Oct 2019</div></div>
                 <div><div class="version-label">REVEL</div> <div class="number">v1.3</div></div>
                 <div><div class="version-label">FreeBayes</div><div class="number">v1.3.1</div></div>
                 <div><div class="version-label">Samtools</div><div class="number">
                 1.9</div></div>
                 <div><div class="version-label">Tabix</div><div class="number">1.9</div></div>
                 <div><div class="version-label">vt subset, normalize</div><div class="number">v0.57721</div></div>
-                <div><div class="version-label">gnomAD </div><div class="number">v2.1 for GRCh37, v4 for GRCh38 </div></div>
-                <div><div class="version-label">ACMG Genes</div> <div class="number">v3.2</div></div>
 
 
               </div>
@@ -1329,7 +1347,7 @@ nav.toolbar, nav.v-toolbar
               2078-9. [PMID: <a href="http://www.ncbi.nlm.nih.gov/pubmed/19505943">19505943</a>]
 
               <div class="citation-title">Bamtools</div>
-              BamTools: a C++ API and toolkit for analyzing and managing BAM files</span>. Bioinformatics 2011;27:1691-1692.
+              BamTools: a C++ API and toolkit for analyzing and managing BAM files. Bioinformatics 2011;27:1691-1692.
               <a href="/cgi/ijlink?linkType=ABST&amp;journalCode=bioinfo&amp;resid=27/12/1691" class="cit-ref-sprinkles cit-ref-sprinkles-ijlinks"><span class="cit-reflinks-abstract">Abstract</span><span class="cit-sep cit-reflinks-variant-name-sep">/</span><span class="cit-reflinks-full-text"><span class="free-full-text">FREE </span>Full Text</span></a>
 
               <div class="citation-title">vt</div>
@@ -1490,6 +1508,7 @@ export default {
     settingsCoverageOnly: null,
     settingsGeneSourceOnly: null,
     analysisModel: null,
+    project: null
   },
   data () {
     let self = this;
@@ -1950,7 +1969,6 @@ export default {
     onShowAlertsForGene: function(geneName) {
       this.$emit('show-alerts-for-gene', geneName)
     }
-
   },
   created: function() {
   },

client/app/components/viz/Navigation.vue

@@ -806,21 +806,24 @@ export default {
       }
     },
     depthVizRegionGlyph: function(exon, regionGroup, regionX, modelName) {
-      let exonId = 'exon' + exon.exon_number.replace("/", "-");
-      if (regionGroup.select("g#" + exonId).empty()) {
-        regionGroup.append('g')
-              .attr("id", exonId)
-              .attr('class',      'region-glyph coverage-problem-glyph')
-              .attr("modelName", modelName)
-              .attr('transform',  'translate(' + (regionX - 6) + ',-6)')
-              .data([exon])
-              .append('use')
-              .attr('height',     '16')
-              .attr('width',      '16')
-              .attr('href', '#coverage-problem-symbol')
-              .attr('xlink','http://www.w3.org/1999/xlink')
-              .data([exon])
-                .attr("modelName", this.sampleModel.name);
+      if (exon.hasOwnProperty('exon_number') && exon.exon_number && exon.exon_number.length > 0) {
+        let exonId = 'exon' + exon.exon_number.replace("/", "-");
+        if (regionGroup.select("g#" + exonId).empty()) {
+          regionGroup.append('g')
+                .attr("id", exonId)
+                .attr('class',      'region-glyph coverage-problem-glyph')
+                .attr("modelName", modelName)
+                .attr('transform',  'translate(' + (regionX - 6) + ',-6)')
+                .data([exon])
+                .append('use')
+                .attr('height',     '16')
+                .attr('width',      '16')
+                .attr('href', '#coverage-problem-symbol')
+                .attr('xlink','http://www.w3.org/1999/xlink')
+                .data([exon])
+                  .attr("modelName", this.sampleModel.name);
+        }
+        
       }
     },
     onVariantClick: function(variant, model) {
@@ -1086,19 +1089,22 @@ export default {
         const matchingVariants = self.sampleModel.loadedVariants.features.filter(function(v) {
           return v.start === variant.start && v.alt === variant.alt && v.ref === variant.ref;
         })
+        let theDepthSource = "genotype_depth"
         if (matchingVariants.length > 0) {
-          theDepth = matchingVariants[0].bamDepth;
-          // If samtools mpileup didn't return coverage for this position, use the variant's depth field
+          theDepth = matchingVariants[0].genotypeDepth;
+          // If we don't have the read count from the genotype depth on the variant,
+          // use the average base coverage (from samtools pileup) that was calculated for this position
           if (theDepth == null || theDepth === '') {
-            theDepth = matchingVariants[0].genotypeDepth;
+            theDepth = matchingVariants[0].bamDepth;
+            theDepthSource = "average_base_coverage"
           }
           if (matchingVariants[0].genotype && matchingVariants[0].genotype.altCount) {
             theAltCount = matchingVariants[0].genotype.altCount;
           }
         }
         // If we have the exact depth for this variant, show it.  Otherwise, we will show
         // the calculated (binned, averaged) depth at this position.
-        let currentPoint = {pos: variant.start, depth: theDepth, altCount: theAltCount}
+        let currentPoint = {pos: variant.start, depth: theDepth, depthSource: theDepthSource}
         self.$refs.depthVizRef.showCurrentPoint(currentPoint);
       }
       self.showCoverageCircleOther(variant);

client/app/components/viz/VariantAllCard.vue

@@ -1772,19 +1772,25 @@ export default {
     },
 
     depthVizRegionGlyph: function(exon, regionGroup, regionX) {
-      var exonId = 'exon' + exon.exon_number.replace("/", "-");
-      if (regionGroup.select("g#" + exonId).empty()) {
-        regionGroup.append('g')
-              .attr("id", exonId)
-              .attr('class',      'region-glyph coverage-problem-glyph')
-              .attr('transform',  'translate(' + (regionX - 6) + ',-25)')
-              .data([exon])
-              .append('use')
-              .attr('height',     '12')
-              .attr('width',      '12')
-              .attr('href', '#coverage-problem-symbol')
-              .attr('xlink','http://www.w3.org/1999/xlink')
-              .data([exon]);
+      if (exon.hasOwnProperty('exon_number')) {
+        var exonId = 'exon' + exon.exon_number.replace("/", "-");
+        if (exonId && exonId.length > 0) {
+          if (regionGroup.select("g#" + exonId).empty()) {
+            regionGroup.append('g')
+                .attr("id", exonId)
+                .attr('class',      'region-glyph coverage-problem-glyph')
+                .attr('transform',  'translate(' + (regionX - 6) + ',-25)')
+                .data([exon])
+                .append('use')
+                .attr('height',     '12')
+                .attr('width',      '12')
+                .attr('href', '#coverage-problem-symbol')
+                .attr('xlink','http://www.w3.org/1999/xlink')
+                .data([exon]);
+          }
+          
+        }
+        
       }
     },
     getExonClass: function(exon, i) {

client/app/components/viz/VariantInspectCard.vue

@@ -57,10 +57,10 @@ export default function lineD3() {
     return { x: xn, y: yn };
   }
 
-  var formatCircleText = function(pos, depth) {
-        return pos + ',' + depth;
+  var formatCircleText = function(pos, depth, depthSource) {
+        return pos + ',' + depth + " " + (depthSource && depthSource == "average_base_coverage" ? "x" : " reads");
   }
-  var showCircle = function(start, theDepth, altCount) {
+  var showCircle = function(start, theDepth, altCount, depthSource) {
     if (container == null) {
       return;
     }
@@ -93,7 +93,7 @@ export default function lineD3() {
       if (theDepth == null || theDepth == "") {
         theDepth = depthy.toString();
       }
-      var circleText = formatCircleText(posx, theDepth);
+      var circleText = formatCircleText(posx, theDepth, depthSource);
       if (debug) {
         circleText += ' ' + posx + ':' + depthy + ' ' + invertedx + ':' + invertedy;
       }