Add partner choice to frontend

README.md

@@ -42,19 +42,21 @@ These parameters are optional and may be omitted using the default values:
 | *breakpointTolerance* | If grouping is enabled, this is the maximum distance where two breakpoints are considered similar. | `3` |
 | *csvDelimiter* | Character that delimits csv columns. | `";"` |
 | *collectionDelimiter* | A single cell in a csv table may have multiple values. These values are seperated by this character. |`","` |
+| *partnerFile* | CSV file containing partnering information (i.e., control-tumor pairs, trios). When used, VIPER offers to inspect the partner samples as well as the sample the respective variant was called in. | `null` |
+| *partnerDelimiter* | Delimiter used when reading partnering information. | `","` |
 | *viperPort* | Port that VIPER listens on. | `8090` |
 | *igvPort* | Port that IGV uses to communicate with VIPER | `9090` |
+| *fastaRef* | `.fasta` reference file or IGV reference key (e.g. `hg19`). Set to a `.fasta` file for improved performance.| `"hg19"` |
+| *numPrecomputedSnapshots* | Precompute this number of breakpoint images to minimize visualization waiting time. | `10` |
 | *keepVcfSimple* | Use only mandatory vcf columns and ignore additional INFO and genotype information | `false` |
 | *excludeRefVcfCalls* | Ignore calls that are marked as reference calls. | `true`
 | *igvJar* | Path to IGV jar file. | `"igv.jar"`|
-| *numPrecomputedSnapshots* | Precompute this number of breakpoint images to minimize visualization waiting time. | `10` |
 | *xvfbDisplay* | When using `Xvfb`, use this number as display number. | `1234` |
 | *xvfbWidth* | When using `Xvfb`, create a window with this width. | `1280` |
 | *xvfbHeight* | When using `Xvfb`, create a window with this height. | `1680` |
 | *igvMaxMemory* | Maximum heap size of the IGV process. | `1200` |
 | *xslxExportWindowSize* | When creating `.xlsx` files, this improves memory usage. Only change if exceptions occur during `.xlsx` export. | `1000` |
 | *igvLog* | File containing IGV logs | `igv.log` |
-| *fastaRef* | `.fasta` reference file or IGV reference key (e.g. `hg19`). Set to a `.fasta` file for improved performance.|
 
 ## Examples
 

public/viper/igv-image/igv-image.tpl.html

@@ -18,7 +18,7 @@
   along with VIPER.  If not, see <http://www.gnu.org/licenses/>.
 
 -->
-<h3>Breakpoint:
+<h3>Inspecting:
   <small>
     {{ igvImageController.sample }},
     {{ igvImageController.chr }}

public/viper/pages/inspector/controller.js

@@ -30,11 +30,14 @@ var module = angular.module('de.imi.marw.viper.inspector', [
   Ctrl.index          = null;
   Ctrl.relatedCallIndex = null;
   Ctrl.currentVariant = null;
+  Ctrl.selectedSample = null;
   Ctrl.relatedVariants = [ ];
   Ctrl.columnNames = [ ];
 
   Ctrl.init = init;
   Ctrl.onIndexChange = onIndexChange;
+  Ctrl.getCurrentPartners = getCurrentPartners;
+  Ctrl.getCurrentVariantSample = getCurrentVariantSample;
   Ctrl.variantPropertyToString = VariantTableService.variantPropertyToString;
   Ctrl.sendDecision = sendDecision;
   Ctrl.changeIGVSetting = changeIGVSetting;
@@ -46,17 +49,20 @@ var module = angular.module('de.imi.marw.viper.inspector', [
       VariantTableService.getSize(),
       VariantTableService.getRelatedColumnNames(),
       VariantTableService.getIGVConfiguration(),
-      VariantTableService.getIGVConfigurationHash()
+      VariantTableService.getIGVConfigurationHash(),
+      VariantTableService.getPartnerMap()
     ]).then(function (data) {
 
       var tableSize = data[0];
       var columnNames = data[1];
       var configuration = data[2];
       var configurationHash = data[3];
+      var partnerMap = data[4]
 
       Ctrl.tableSize = tableSize;
       Ctrl.index     = VariantTableService.currentVariantIndex;
       Ctrl.columnNames = columnNames;
+      Ctrl.partnerMap = partnerMap;
 
       Ctrl.configuration = configuration;
       Ctrl.configurationHash = configurationHash;
@@ -80,6 +86,21 @@ var module = angular.module('de.imi.marw.viper.inspector', [
     });
   }
 
+  function getCurrentVariantSample() {
+
+    if (Ctrl.relatedVariants == null || Ctrl.relatedCallIndex == null) return null;
+
+    return Ctrl.relatedVariants[Ctrl.relatedCallIndex].sample
+
+  }
+
+  function getCurrentPartners() {
+
+    if (Ctrl.partnerMap == null) return null;
+
+    return Ctrl.partnerMap[Ctrl.getCurrentVariantSample()] || [];
+  }
+
   function sendDecision (decision) {
 
     var promise = VariantTableService.sendDecision(Ctrl.index, decision);
@@ -94,6 +115,7 @@ var module = angular.module('de.imi.marw.viper.inspector', [
 
   function onRelatedCallIndexChange (sliderId, modelValue) {
     VariantTableService.scheduleSnapshot(Ctrl.index, modelValue);
+    Ctrl.selectedSample = Ctrl.relatedVariants[modelValue].sample;
   }
 
   function onIndexChange () {
@@ -109,6 +131,7 @@ var module = angular.module('de.imi.marw.viper.inspector', [
     ]).then(function (data) {
       Ctrl.currentVariant = data[0];
       Ctrl.relatedVariants = data[1];
+      Ctrl.selectedSample = Ctrl.relatedVariants[0].sample;
 
       var samples = [];
 

public/viper/pages/inspector/inspector.html

@@ -50,9 +50,33 @@ <h3 class="variant-well-header">variants: {{ inspectorCtrl.tableSize }}</h3>
 
       <br>
 
+      <div ng-if="inspectorCtrl.getCurrentPartners().length > 0">
+
+        <strong>Select sample to inspect:</strong>
+
+        <br>
+
+        <div class="radio">
+          <label>
+            <input type="radio" ng-model="inspectorCtrl.selectedSample" value="{{ inspectorCtrl.getCurrentVariantSample() }}">
+            {{ inspectorCtrl.getCurrentVariantSample() }}
+            <small><em>called</em></small>
+          </label>
+        </div>
+
+        <div class="radio" ng-repeat="partnerSample in inspectorCtrl.getCurrentPartners()">
+          <label>
+            <input type="radio" ng-model="inspectorCtrl.selectedSample" value="{{ partnerSample }}">
+            {{ partnerSample }}
+            <small><em>partner</em></small>
+          </label>
+        </div>
+
+      </div>
+
       <div ng-if="inspectorCtrl.relatedVariants.length > 1">
 
-        <strong>Select related call to inspect:</strong>
+        <strong>Select related call in group to inspect:</strong>
 
         <rzslider
           rz-slider-model="inspectorCtrl.relatedCallIndex"
@@ -196,7 +220,7 @@ <h4>Visualization settings</h4>
 
           <div class="col-md-6">
             <igv-image
-              sample="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['sample']"
+              sample="inspectorCtrl.selectedSample"
               chr="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['chr1']"
               pos="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['bp1']"
               igv-configuration-hash="inspectorCtrl.configurationHash">
@@ -205,7 +229,7 @@ <h4>Visualization settings</h4>
 
           <div class="col-md-6">
             <igv-image
-              sample="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['sample']"
+              sample="inspectorCtrl.selectedSample"
               chr="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['chr2']"
               pos="inspectorCtrl.relatedVariants[inspectorCtrl.relatedCallIndex]['bp2']"
               igv-configuration-hash="inspectorCtrl.configurationHash">

public/viper/variant-table/VariantTableService.js

@@ -39,6 +39,7 @@ var module = angular.module('de.imi.marw.viper.variant-table.service', [
   Service.getTableRange = getTableRange;
   Service.getTableRow = getTableRow;
   Service.getUnfilteredSize = getUnfilteredSize;
+  Service.getPartnerMap = getPartnerMap;
   Service.saveProgress = saveProgress;
   Service.scheduleSnapshot = scheduleSnapshot;
   Service.searchStringColumn = searchStringColumn
@@ -140,6 +141,10 @@ var module = angular.module('de.imi.marw.viper.variant-table.service', [
     return promise;
   }
 
+  function getPartnerMap() {
+    return performRequest("/api/snapshots/partners");
+  }
+
   function scheduleSnapshot(index, relatedCallIndex) {
 
     var promise = $http.post("/api/snapshots/take-snapshot", {}, {

src/main/java/de/imi/marw/viper/api/routes/SnapshotRoutes.java

@@ -129,8 +129,19 @@ private Object takeSnapshot(Request req, Response res) {
                 int bp1 = ((Double) relatedCall.get(VariantTable.BP1_COLUMN_NAME)).intValue();
                 int bp2 = ((Double) relatedCall.get(VariantTable.BP2_COLUMN_NAME)).intValue();
 
-                this.igv.scheduleSnapshot(sample, chr1, bp1, i == queryIndex && j == selectedRelatedCall);
-                this.igv.scheduleSnapshot(sample, chr2, bp2, i == queryIndex && j == selectedRelatedCall);
+                boolean isCurrentSnapshot = i == queryIndex && j == selectedRelatedCall;
+
+                this.igv.scheduleSnapshot(sample, chr1, bp1, isCurrentSnapshot);
+                this.igv.scheduleSnapshot(sample, chr2, bp2, isCurrentSnapshot);
+
+                List<String> relatedPartners = this.partners.getPartners(sample);
+
+                for (String partner : relatedPartners) {
+
+                    this.igv.scheduleSnapshot(partner, chr1, bp1, isCurrentSnapshot);
+                    this.igv.scheduleSnapshot(partner, chr2, bp2, isCurrentSnapshot);
+
+                }
 
             }
         }

src/main/java/de/imi/marw/viper/visualization/SamplePartners.java

@@ -55,7 +55,7 @@ private SamplePartners(Map<String, List<String>> samplePartnerMap) {
     }
 
     public Map<String, List<String>> getMap() {
-        return Collections.unmodifiableMap(samplePartnerMap);
+        return Collections.unmodifiableMap(this.samplePartnerMap);
     }
 
     public List<String> getPartners(String sample) {