@jbrowse/plugin-variants 4.0.4 → 4.1.3

package/esm/index.js

@@ -1,14 +1,19 @@
 import Plugin from '@jbrowse/core/Plugin';
 import ChordVariantDisplayF from "./ChordVariantDisplay/index.js";
+import LDDisplayF from "./LDDisplay/index.js";
+import LDRendererF from "./LDRenderer/index.js";
+import LDTrackF from "./LDTrack/index.js";
 import LinearVariantDisplayF from "./LinearVariantDisplay/index.js";
 import MultiLinearVariantDisplayF from "./MultiLinearVariantDisplay/index.js";
 import LinearVariantMatrixDisplayF from "./MultiLinearVariantMatrixDisplay/index.js";
 import LinearVariantMatrixRendererF from "./MultiLinearVariantMatrixRenderer/index.js";
 import MultiVariantRendererF from "./MultiLinearVariantRenderer/index.js";
+import PlinkLDAdapterF from "./PlinkLDAdapter/index.js";
 import SplitVcfTabixAdapterF from "./SplitVcfTabixAdapter/index.js";
 import StructuralVariantChordRendererF from "./StructuralVariantChordRenderer/index.js";
 import VariantFeatureWidgetF from "./VariantFeatureWidget/index.js";
 import { MultiVariantClusterGenotypeMatrix } from "./VariantRPC/MultiVariantClusterGenotypeMatrix.js";
+import { MultiVariantGetFeatureDetails } from "./VariantRPC/MultiVariantGetFeatureDetails.js";
 import { MultiVariantGetGenotypeMatrix } from "./VariantRPC/MultiVariantGetGenotypeMatrix.js";
 import { MultiVariantGetSimplifiedFeatures } from "./VariantRPC/MultiVariantGetSimplifiedFeatures.js";
 import { MultiVariantGetSources } from "./VariantRPC/MultiVariantGetSources.js";
@@ -16,18 +21,23 @@ import VariantTrackF from "./VariantTrack/index.js";
 import VcfAdapterF from "./VcfAdapter/index.js";
 import ExtensionPointsF from "./VcfExtensionPoints/index.js";
 import VcfTabixAdapterF from "./VcfTabixAdapter/index.js";
+import { calculateAlleleCounts, calculateMinorAlleleFrequency, } from "./shared/minorAlleleFrequencyUtils.js";
 export default class VariantsPlugin extends Plugin {
     name = 'VariantsPlugin';
     install(pluginManager) {
         VcfAdapterF(pluginManager);
         VcfTabixAdapterF(pluginManager);
         SplitVcfTabixAdapterF(pluginManager);
+        PlinkLDAdapterF(pluginManager);
         VariantFeatureWidgetF(pluginManager);
         VariantTrackF(pluginManager);
+        LDTrackF(pluginManager);
         ExtensionPointsF(pluginManager);
         LinearVariantDisplayF(pluginManager);
         LinearVariantMatrixDisplayF(pluginManager);
         MultiLinearVariantDisplayF(pluginManager);
+        LDDisplayF(pluginManager);
+        LDRendererF(pluginManager);
         MultiVariantRendererF(pluginManager);
         LinearVariantMatrixRendererF(pluginManager);
         StructuralVariantChordRendererF(pluginManager);
@@ -36,6 +46,19 @@ export default class VariantsPlugin extends Plugin {
         pluginManager.addRpcMethod(() => new MultiVariantGetGenotypeMatrix(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantClusterGenotypeMatrix(pluginManager));
         pluginManager.addRpcMethod(() => new MultiVariantGetSimplifiedFeatures(pluginManager));
+        pluginManager.addRpcMethod(() => new MultiVariantGetFeatureDetails(pluginManager));
+    }
+    configure(pluginManager) {
+        const { jexl } = pluginManager;
+        const splitCache = {};
+        jexl.addFunction('maf', (feature) => {
+            const genotypes = feature.get('genotypes');
+            if (!genotypes) {
+                return 0;
+            }
+            const alleleCounts = calculateAlleleCounts(genotypes, splitCache);
+            return calculateMinorAlleleFrequency(alleleCounts);
+        });
     }
 }
 export { default as VcfFeature } from "./VcfFeature/index.js";