@jbrowse/plugin-bed 4.2.0 → 4.3.0

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -109,8 +109,9 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                 });
                 const aggr = data[aggregateField];
                 const aggrIsNotNone = aggr && aggr !== 'none';
-                if (aggrIsNotNone && !parentAggregation[aggr]) {
-                    parentAggregation[aggr] = [];
+                const aggrKey = typeof aggr === 'string' ? aggr : `${aggr}`;
+                if (aggrIsNotNone && !parentAggregation[aggrKey]) {
+                    parentAggregation[aggrKey] = [];
                 }
                 const { uniqueId, type, chrom, chromStart, chromEnd, description, chromStarts: chromStarts2, blockStarts: blockStarts2, blockSizes: blockSizes2, score: score2, blockCount, thickStart, thickEnd, strand, ...rest } = data;
                 const f = featureData2({
@@ -118,14 +119,14 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                     scoreColumn,
                     splitLine,
                     parser,
-                    uniqueId,
+                    uniqueId: uniqueId,
                     start: feat.start,
                     end: feat.end,
                     refName: query.refName,
                     disableGeneHeuristic,
                 });
                 if (aggrIsNotNone) {
-                    parentAggregation[aggr].push(f);
+                    parentAggregation[aggrKey].push(f);
                     parentAggregationFlat.push(f);
                 }
                 else {

package/esm/GuessAdapter/index.js

@@ -12,7 +12,7 @@ export default function GuessAdapterF(pluginManager) {
                 };
             }
             else if (testAdapter(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
-                testAdapter(fileName, /\.bigBed?$/i, adapterHint, 'BigBedAdapter')) {
+                testAdapter(fileName, /\.bigbed$/i, adapterHint, 'BigBedAdapter')) {
                 return {
                     type: 'BigBedAdapter',
                     bigBedLocation: file,
@@ -40,7 +40,8 @@ export default function GuessAdapterF(pluginManager) {
                     },
                 };
             }
-            else if (testAdapter(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
+            else if (testAdapter(fileName, /\.bedmethyl\.gz$/i, adapterHint, 'BedTabixAdapter') ||
+                testAdapter(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
                 return {
                     type: 'BedTabixAdapter',
                     bedGzLocation: file,
@@ -55,11 +56,16 @@ export default function GuessAdapterF(pluginManager) {
             }
         };
     });
-    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName) => {
+    pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => (adapterName, file) => {
+        if (adapterName === 'BedTabixAdapter' &&
+            file &&
+            /\.bedmethyl\.gz$/i.test(getFileName(file))) {
+            return 'MultiQuantitativeTrack';
+        }
         return ({
             BedpeAdapter: 'VariantTrack',
             BedGraphAdapter: 'QuantitativeTrack',
             BedGraphTabixAdapter: 'QuantitativeTrack',
-        }[adapterName] || trackTypeGuesser(adapterName));
+        }[adapterName] || trackTypeGuesser(adapterName, file));
     });
 }

package/esm/generateRepeatMaskerFeature.d.ts

@@ -1,4 +1,4 @@
-export declare function isRepeatMaskerDescriptionField(desc?: string): desc is string;
+export declare function isRepeatMaskerDescriptionField(desc?: unknown): desc is string;
 export declare function generateRepeatMaskerFeature({ uniqueId, refName, start, end, description, ...rest }: {
     uniqueId: string;
     refName: string;

package/esm/generateRepeatMaskerFeature.js

@@ -1,6 +1,11 @@
 export function isRepeatMaskerDescriptionField(desc) {
-    const ret = desc?.trim().split(' ');
-    return [0, 1, 2, 3, 5, 6].every(s => ret?.[s] !== undefined ? !Number.isNaN(+ret[s]) : false);
+    if (typeof desc !== 'string') {
+        return false;
+    }
+    else {
+        const ret = desc.trim().split(' ');
+        return [0, 1, 2, 3, 5, 6].every(s => ret[s] !== undefined ? !Number.isNaN(+ret[s]) : false);
+    }
 }
 function makeRepeatTrackDescription(description) {
     if (isRepeatMaskerDescriptionField(description)) {

package/esm/generateUcscTranscript.d.ts

@@ -1,9 +1,9 @@
 import type { MinimalFeature } from './types.ts';
 export declare function isUcscTranscript({ thickStart, blockCount, strand, }: {
-    thickStart?: number;
-    blockCount?: number;
+    thickStart?: unknown;
+    blockCount?: unknown;
     strand?: number;
-}): boolean | 0 | undefined;
+}): boolean;
 interface UcscTranscriptInput {
     uniqueId: string;
     strand?: number;

package/esm/generateUcscTranscript.js

@@ -1,5 +1,7 @@
 export function isUcscTranscript({ thickStart, blockCount, strand, }) {
-    return thickStart && blockCount && strand !== 0;
+    return (typeof thickStart === 'number' &&
+        typeof blockCount === 'number' &&
+        strand !== 0);
 }
 function calculatePhasesFromCds(cdsRegions, strand) {
     const sorted = [...cdsRegions].sort((a, b) => strand > 0 ? a.start - b.start : b.start - a.start);

package/esm/util.js

@@ -98,7 +98,7 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             end,
         });
     }
-    if (isRepeatMaskerDescriptionField(rest.description)) {
+    else if (isRepeatMaskerDescriptionField(rest.description)) {
         const { chromStarts: _4, blockSizes: _5, blockStarts: _6, blockCount: _7, thickStart: _8, thickEnd: _9, description, ...rest2 } = rest;
         return generateRepeatMaskerFeature({
             ...rest2,
@@ -112,7 +112,7 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             subfeatures,
         });
     }
-    if (!disableGeneHeuristic &&
+    else if (!disableGeneHeuristic &&
         subfeatures &&
         isUcscTranscript({
             strand,
@@ -132,16 +132,18 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             thickEnd: rest.thickEnd,
         });
     }
-    return {
-        ...rest,
-        uniqueId,
-        score,
-        start,
-        end,
-        strand,
-        refName,
-        subfeatures,
-    };
+    else {
+        return {
+            ...rest,
+            uniqueId,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            subfeatures,
+        };
+    }
 }
 export function arrayify(f) {
     if (f === undefined) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "4.2.0",
+  "version": "4.3.0",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -23,12 +23,12 @@
   "dependencies": {
     "@flatten-js/interval-tree": "^2.0.3",
     "@gmod/bbi": "^9.0.9",
-    "@gmod/bed": "^2.1.10",
-    "@gmod/tabix": "^3.3.1",
+    "@gmod/bed": "^2.2.1",
+    "@gmod/tabix": "^3.3.3",
     "@jbrowse/mobx-state-tree": "^5.6.0",
-    "mobx": "^6.15.0",
+    "mobx": "^6.15.3",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.2.0"
+    "@jbrowse/core": "^4.3.0"
   },
   "publishConfig": {
     "access": "public"