@jbrowse/plugin-bed 4.1.13 → 4.1.14

package/esm/BedAdapter/BedAdapter.js

@@ -85,6 +85,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
             return undefined;
         }
         const names = await this.getNames();
+        const disableGeneHeuristic = this.getConf('disableGeneHeuristic');
         const intervalTree = new IntervalTree();
         for (let i = 0; i < lines.length; i++) {
             const line = lines[i];
@@ -98,6 +99,7 @@ export default class BedAdapter extends BaseFeatureDataAdapter {
                 parser,
                 uniqueId,
                 names,
+                disableGeneHeuristic,
             }));
             intervalTree.insert([feat.get('start'), feat.get('end')], feat);
         }

package/esm/BedAdapter/configSchema.d.ts

@@ -37,5 +37,10 @@ declare const BedAdapter: import("@jbrowse/core/configuration/configurationSchem
         description: string;
         defaultValue: number;
     };
+    disableGeneHeuristic: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BedAdapter;

package/esm/BedAdapter/configSchema.js

@@ -39,6 +39,11 @@ const BedAdapter = ConfigurationSchema('BedAdapter', {
         description: 'The column to use as a "end" attribute',
         defaultValue: 2,
     },
+    disableGeneHeuristic: {
+        type: 'boolean',
+        description: 'Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)',
+        defaultValue: false,
+    },
 }, {
     explicitlyTyped: true,
     preProcessSnapshot: snap => {

package/esm/BedTabixAdapter/BedTabixAdapter.js

@@ -76,6 +76,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
             const colStart = columnNumbers.start - 1;
             const colEnd = columnNumbers.end - 1;
             const names = await this.getNames();
+            const disableGeneHeuristic = this.getConf('disableGeneHeuristic');
             let start = performance.now();
             checkStopToken(stopToken);
             await updateStatus('Downloading features', statusCallback, () => this.bed.getLines(query.refName, query.start, query.end, {
@@ -93,6 +94,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
                         parser: this.parser,
                         uniqueId: `${this.id}-${fileOffset}`,
                         names,
+                        disableGeneHeuristic,
                     })));
                 },
                 stopToken,

package/esm/BedTabixAdapter/configSchema.d.ts

@@ -35,5 +35,10 @@ declare const BedTabixAdapter: import("@jbrowse/core/configuration/configuration
         description: string;
         defaultValue: string;
     };
+    disableGeneHeuristic: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BedTabixAdapter;

package/esm/BedTabixAdapter/configSchema.js

@@ -38,6 +38,11 @@ const BedTabixAdapter = ConfigurationSchema('BedTabixAdapter', {
         description: 'The autoSql definition for the data fields in the file',
         defaultValue: '',
     },
+    disableGeneHeuristic: {
+        type: 'boolean',
+        description: 'Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)',
+        defaultValue: false,
+    },
 }, {
     explicitlyTyped: true,
     preProcessSnapshot: snap => {

package/esm/BigBedAdapter/BigBedAdapter.js

@@ -86,6 +86,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
         const { statusCallback = () => { } } = opts;
         const scoreColumn = this.getConf('scoreColumn');
         const aggregateField = this.getConf('aggregateField');
+        const disableGeneHeuristic = this.getConf('disableGeneHeuristic');
         const { parser, bigbed } = await updateStatus('Downloading header', statusCallback, () => this.configure(opts));
         const feats = await updateStatus('Downloading features', statusCallback, () => bigbed.getFeatures(query.refName, query.start, query.end, {
             basesPerSpan: query.end - query.start,
@@ -121,6 +122,7 @@ export default class BigBedAdapter extends BaseFeatureDataAdapter {
                     start: feat.start,
                     end: feat.end,
                     refName: query.refName,
+                    disableGeneHeuristic,
                 });
                 if (aggrIsNotNone) {
                     parentAggregation[aggr].push(f);

package/esm/BigBedAdapter/configSchema.d.ts

@@ -16,5 +16,10 @@ declare const BigBedAdapter: import("@jbrowse/core/configuration/configurationSc
         description: string;
         defaultValue: string;
     };
+    disableGeneHeuristic: {
+        type: string;
+        description: string;
+        defaultValue: boolean;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default BigBedAdapter;

package/esm/BigBedAdapter/configSchema.js

@@ -18,6 +18,11 @@ const BigBedAdapter = ConfigurationSchema('BigBedAdapter', {
         description: 'An attribute to aggregate features with',
         defaultValue: 'geneName2',
     },
+    disableGeneHeuristic: {
+        type: 'boolean',
+        description: 'Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)',
+        defaultValue: false,
+    },
 }, {
     explicitlyTyped: true,
     preProcessSnapshot: snap => {

package/esm/util.d.ts

@@ -15,7 +15,7 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
     refName: string;
     type: string;
 }[];
-export declare function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, }: {
+export declare function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, disableGeneHeuristic, }: {
     line: string;
     colRef: number;
     colStart: number;
@@ -24,6 +24,7 @@ export declare function featureData({ line, colRef, colStart, colEnd, scoreColum
     parser: BED;
     uniqueId: string;
     names?: string[];
+    disableGeneHeuristic?: boolean;
 }): FeatureData;
 interface FeatureData {
     uniqueId: string;
@@ -36,7 +37,7 @@ interface FeatureData {
     subfeatures?: MinimalFeature[];
     [key: string]: unknown;
 }
-export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
+export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, disableGeneHeuristic, }: {
     splitLine: string[];
     refName: string;
     start: number;
@@ -45,6 +46,7 @@ export declare function featureData2({ splitLine, refName, start, end, parser, u
     uniqueId: string;
     scoreColumn: string;
     names?: string[];
+    disableGeneHeuristic?: boolean;
 }): FeatureData;
 export declare function arrayify(f?: string | number[]): number[] | undefined;
 export {};

package/esm/util.js

@@ -45,7 +45,7 @@ export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount,
     }
     return subfeatures;
 }
-export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, }) {
+export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, disableGeneHeuristic, }) {
     const splitLine = line.split('\t');
     const refName = splitLine[colRef];
     const start = Number.parseInt(splitLine[colStart], 10);
@@ -59,6 +59,7 @@ export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parse
         uniqueId,
         scoreColumn,
         names,
+        disableGeneHeuristic,
     });
 }
 function parseStrand(strand) {
@@ -70,7 +71,7 @@ function parseStrand(strand) {
     }
     return 0;
 }
-export function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
+export function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, disableGeneHeuristic, }) {
     const data = names
         ? defaultParser(names, splitLine)
         : parser.parseLine(splitLine, { uniqueId });
@@ -111,7 +112,8 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             subfeatures,
         });
     }
-    if (subfeatures &&
+    if (!disableGeneHeuristic &&
+        subfeatures &&
         isUcscTranscript({
             strand,
             blockCount: rest.blockCount,

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "4.1.13",
+  "version": "4.1.14",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -28,7 +28,7 @@
     "@jbrowse/mobx-state-tree": "^5.5.0",
     "mobx": "^6.15.0",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.1.13"
+    "@jbrowse/core": "^4.1.14"
   },
   "publishConfig": {
     "access": "public"