@jbrowse/plugin-bed 4.3.0 → 5.0.0-beta.1

package/esm/generateUcscTranscript.js

@@ -1,35 +1,52 @@
-export function isUcscTranscript({ thickStart, blockCount, strand, }) {
-    return (typeof thickStart === 'number' &&
-        typeof blockCount === 'number' &&
-        strand !== 0);
+// type guard: narrows input fields to required + non-zero when true
+// strand===0 means unstranded — likely not a gene
+export function isUcscTranscript(input) {
+    return (input.thickStart !== undefined &&
+        input.thickEnd !== undefined &&
+        input.thickStart !== input.thickEnd &&
+        input.blockCount !== undefined &&
+        input.blockCount > 0 &&
+        input.strand !== undefined &&
+        input.strand !== 0);
 }
+// phase = (3 - cumulative_cds_width % 3) % 3, computed in transcriptional order
 function calculatePhasesFromCds(cdsRegions, strand) {
     const sorted = [...cdsRegions].sort((a, b) => strand > 0 ? a.start - b.start : b.start - a.start);
     const phaseMap = new Map();
     let cumulativeWidth = 0;
     for (const cds of sorted) {
-        const phase = (3 - (cumulativeWidth % 3)) % 3;
-        phaseMap.set(cds.start, phase);
+        phaseMap.set(cds.start, (3 - (cumulativeWidth % 3)) % 3);
         cumulativeWidth += cds.end - cds.start;
     }
     return phaseMap;
 }
+// convert UCSC exonFrames (0,1,2) to GFF phase: frame 0→0, frame 1→2, frame 2→1
+// UCSC frame = bases from start of codon; GFF phase = bases to skip to reach next codon
+// https://genome.ucsc.edu/FAQ/FAQformat.html#format1 (bigGenePred exonFrames)
+// https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md (phase)
 function frameToPhase(frame) {
     return (3 - frame) % 3;
 }
+function parseFrames(frames) {
+    return typeof frames === 'string'
+        ? frames.replace(/,$/, '').split(',').map(Number)
+        : frames;
+}
 export function generateUcscTranscript(data) {
-    const { strand = 0, uniqueId, start, end, ...rest } = data;
-    const { subfeatures: oldSubfeatures, thickStart, thickEnd, refName, chrom: _1, chromStart: _2, chromEnd: _3, chromStarts: _4, blockStarts: _5, blockSizes: _6, blockCount: _7, ...rest2 } = rest;
-    const exonFrames = (rest2.exonFrames ?? rest2._exonFrames);
+    const { strand, uniqueId, start, end, thickStart, thickEnd, refName, subfeatures: oldSubfeatures, chrom, chromStart, chromEnd, chromStarts, blockStarts, blockSizes, blockCount, ...rest } = data;
+    // exonFrames from bigGenePred - the @gmod/bed parser returns it in genomic order.
+    // _exonFrames fallback supports BED files that use the underscore-prefixed column
+    // name, which the parser leaves as raw text because it is not a standard column.
+    const exonFrames = parseFrames(rest.exonFrames ?? rest._exonFrames);
     const feats = oldSubfeatures
         .filter(child => child.type === 'block')
         .sort((a, b) => a.start - b.start);
     const fiveUTR = strand > 0 ? 'five_prime_UTR' : 'three_prime_UTR';
     const threeUTR = strand > 0 ? 'three_prime_UTR' : 'five_prime_UTR';
-    const { cdsEndStat, cdsStartStat } = rest2;
+    const { cdsEndStat, cdsStartStat } = rest;
     if (cdsStartStat === 'none' && cdsEndStat === 'none') {
         return {
-            ...rest2,
+            ...rest,
             uniqueId,
             strand,
             type: 'transcript',
@@ -39,15 +56,15 @@ export function generateUcscTranscript(data) {
             subfeatures: feats.map(e => ({ ...e, type: 'exon' })),
         };
     }
+    // If exonFrames not available, calculate phases from CDS regions
     let calculatedPhases;
     if (!exonFrames) {
         const cdsRegions = [];
         for (const block of feats) {
-            const { start, end } = block;
-            if (thickStart < end && thickEnd > start) {
+            if (thickStart < block.end && thickEnd > block.start) {
                 cdsRegions.push({
-                    start: Math.max(start, thickStart),
-                    end: Math.min(end, thickEnd),
+                    start: Math.max(block.start, thickStart),
+                    end: Math.min(block.end, thickEnd),
                 });
             }
         }
@@ -55,20 +72,28 @@ export function generateUcscTranscript(data) {
     }
     const subfeatures = [];
     for (const [i, feat] of feats.entries()) {
-        const block = feat;
-        const { start, end } = block;
-        if (thickStart >= end) {
-            subfeatures.push({ type: fiveUTR, start, end, refName });
+        const { start: bStart, end: bEnd } = feat;
+        if (thickStart >= bEnd) {
+            // entire block is 5' UTR
+            subfeatures.push({ type: fiveUTR, start: bStart, end: bEnd, refName });
         }
-        else if (thickEnd <= start) {
-            subfeatures.push({ type: threeUTR, start, end, refName });
+        else if (thickEnd <= bStart) {
+            // entire block is 3' UTR
+            subfeatures.push({ type: threeUTR, start: bStart, end: bEnd, refName });
         }
         else {
-            if (start < thickStart) {
-                subfeatures.push({ type: fiveUTR, start, end: thickStart, refName });
+            // block overlaps CDS region - may have UTR on either side
+            if (bStart < thickStart) {
+                subfeatures.push({
+                    type: fiveUTR,
+                    start: bStart,
+                    end: thickStart,
+                    refName,
+                });
             }
-            const cdsStart = Math.max(start, thickStart);
-            const cdsEnd = Math.min(end, thickEnd);
+            const cdsStart = Math.max(bStart, thickStart);
+            const cdsEnd = Math.min(bEnd, thickEnd);
+            // Get phase from exonFrames (with conversion) or calculated phases
             let phase = 0;
             if (exonFrames) {
                 const frame = exonFrames[i];
@@ -86,13 +111,18 @@ export function generateUcscTranscript(data) {
                 end: cdsEnd,
                 refName,
             });
-            if (end > thickEnd) {
-                subfeatures.push({ type: threeUTR, start: thickEnd, end, refName });
+            if (bEnd > thickEnd) {
+                subfeatures.push({
+                    type: threeUTR,
+                    start: thickEnd,
+                    end: bEnd,
+                    refName,
+                });
             }
         }
     }
     return {
-        ...rest2,
+        ...rest,
         uniqueId,
         strand,
         type: 'mRNA',

package/esm/index.d.ts

@@ -1,5 +1,7 @@
 import Plugin from '@jbrowse/core/Plugin';
 import type PluginManager from '@jbrowse/core/PluginManager';
+export { default as BedTabixAdapter } from './BedTabixAdapter/BedTabixAdapter.ts';
+export { default as bedTabixConfigSchema } from './BedTabixAdapter/configSchema.ts';
 export default class BedPlugin extends Plugin {
     name: string;
     install(pluginManager: PluginManager): void;

package/esm/index.js

@@ -1,20 +1,22 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BedAdapterF from "./BedAdapter/index.js";
-import BedGraphAdapterF from "./BedGraphAdapter/index.js";
-import BedGraphTabixAdapterF from "./BedGraphTabixAdapter/index.js";
-import BedTabixAdapterF from "./BedTabixAdapter/index.js";
-import BedpeAdapterF from "./BedpeAdapter/index.js";
-import BigBedAdapterF from "./BigBedAdapter/index.js";
-import GuessAdapterF from "./GuessAdapter/index.js";
+import BedAdapterF from './BedAdapter/index.js';
+import BedGraphAdapterF from './BedGraphAdapter/index.js';
+import BedGraphTabixAdapterF from './BedGraphTabixAdapter/index.js';
+import BedTabixAdapterF from './BedTabixAdapter/index.js';
+import BedpeAdapterF from './BedpeAdapter/index.js';
+import BigBedAdapterF from './BigBedAdapter/index.js';
+import StarFusionAdapterF from './StarFusionAdapter/index.js';
+export { default as BedTabixAdapter } from './BedTabixAdapter/BedTabixAdapter.js';
+export { default as bedTabixConfigSchema } from './BedTabixAdapter/configSchema.js';
 export default class BedPlugin extends Plugin {
     name = 'BedPlugin';
     install(pluginManager) {
         BigBedAdapterF(pluginManager);
         BedAdapterF(pluginManager);
         BedpeAdapterF(pluginManager);
+        StarFusionAdapterF(pluginManager);
         BedTabixAdapterF(pluginManager);
         BedGraphAdapterF(pluginManager);
         BedGraphTabixAdapterF(pluginManager);
-        GuessAdapterF(pluginManager);
     }
 }

package/esm/util.d.ts

@@ -1,5 +1,21 @@
+import BED from '@gmod/bed';
 import type { MinimalFeature } from './types.ts';
-import type BED from '@gmod/bed';
+import type { StatusCallback } from '@jbrowse/core/util';
+export interface FeatureData {
+    uniqueId: string;
+    refName: string;
+    start: number;
+    end: number;
+    strand?: number;
+    score?: number;
+    type?: string;
+    subfeatures?: MinimalFeature[];
+    [key: string]: unknown;
+}
+export declare function bucketBedLines(buffer: Uint8Array, statusCallback?: StatusCallback): {
+    header: string;
+    features: Record<string, string[]>;
+};
 export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
     blockCount: number;
     start: number;
@@ -8,36 +24,27 @@ export declare function makeBlocks({ start, uniqueId, refName, chromStarts, bloc
     chromStarts?: number[];
     blockSizes?: number[];
     blockStarts?: number[];
-}): {
-    uniqueId: string;
-    start: number;
-    end: number;
-    refName: string;
-    type: string;
-}[];
-export declare function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, disableGeneHeuristic, }: {
-    line: string;
+}): MinimalFeature[];
+export declare function parseNamesFromHeader(header: string): string[] | undefined;
+export declare function resolveColumnNames(columnNames: string[], getHeader: () => Promise<string>): Promise<string[] | undefined>;
+export declare function makeParser({ autoSql, columnNames, }: {
+    autoSql?: string;
+    columnNames?: string[];
+}): BED;
+export declare function bedFeatureLocus({ splitLine, colRef, colStart, colEnd, oneBased, hasEndColumn, }: {
+    splitLine: string[];
     colRef: number;
     colStart: number;
     colEnd: number;
-    scoreColumn: string;
-    parser: BED;
-    uniqueId: string;
-    names?: string[];
-    disableGeneHeuristic?: boolean;
-}): FeatureData;
-interface FeatureData {
-    uniqueId: string;
+    oneBased?: boolean;
+    hasEndColumn?: boolean;
+}): {
     refName: string;
     start: number;
     end: number;
-    strand?: number | string;
-    score?: number;
-    type?: string;
-    subfeatures?: MinimalFeature[];
-    [key: string]: unknown;
-}
-export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, disableGeneHeuristic, }: {
+};
+export declare function parseStrand(strand: string | number | undefined): number;
+export declare function featureData({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, disableGeneHeuristic, }: {
     splitLine: string[];
     refName: string;
     start: number;
@@ -48,5 +55,3 @@ export declare function featureData2({ splitLine, refName, start, end, parser, u
     names?: string[];
     disableGeneHeuristic?: boolean;
 }): FeatureData;
-export declare function arrayify(f?: string | number[]): number[] | undefined;
-export {};

package/esm/util.js

@@ -1,31 +1,28 @@
-import { generateBedMethylFeature, isBedMethylFeature, } from "./generateBedMethylFeature.js";
-import { generateRepeatMaskerFeature, isRepeatMaskerDescriptionField, } from "./generateRepeatMaskerFeature.js";
-import { generateUcscTranscript, isUcscTranscript, } from "./generateUcscTranscript.js";
-function defaultParser(fields, splitLine) {
-    const obj = {};
-    let hasBlockCount = false;
-    for (const [i, element] of splitLine.entries()) {
-        const field = fields[i];
-        if (field) {
-            obj[field] = element;
-            if (field === 'blockCount') {
-                hasBlockCount = true;
-            }
+import BED from '@gmod/bed';
+import { parseLineByLine } from '@jbrowse/core/util/parseLineByLine';
+import { generateBedMethylFeature, isBedMethylFeature, } from './generateBedMethylFeature.js';
+import { generateRastairMethylFeature, isRastairMethylFeature, } from './generateRastairMethylFeature.js';
+import { parseRepeatMaskerDescription } from './generateRepeatMaskerFeature.js';
+import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript.js';
+// Heuristically split features and header from a buffered BED file, bucketing
+// data lines by the first tab-separated column (refName).
+export function bucketBedLines(buffer, statusCallback) {
+    const features = {};
+    const headerLines = [];
+    parseLineByLine(buffer, line => {
+        if (line.startsWith('#')) {
+            headerLines.push(line);
         }
-    }
-    if (hasBlockCount) {
-        const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
-        return {
-            ...rest,
-            blockStarts: arrayify(blockStarts),
-            chromStarts: arrayify(chromStarts),
-            blockSizes: arrayify(blockSizes),
-            thickStart: thickStart ? +thickStart : undefined,
-            thickEnd: thickEnd ? +thickEnd : undefined,
-            blockCount: blockCount ? +blockCount : undefined,
-        };
-    }
-    return obj;
+        else if (!line.startsWith('track') && !line.startsWith('browser')) {
+            // 'track'/'browser' are UCSC directive lines, not data (matches
+            // filterBedHeaderLines in spreadsheet-view)
+            const tab = line.indexOf('\t');
+            const refName = tab === -1 ? line : line.slice(0, tab);
+            (features[refName] ??= []).push(line);
+        }
+        return true;
+    }, statusCallback);
+    return { header: headerLines.join('\n'), features };
 }
 export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
     const subfeatures = [];
@@ -45,24 +42,55 @@ export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount,
     }
     return subfeatures;
 }
-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);
-    const end = Number.parseInt(splitLine[colEnd], 10) + (colStart === colEnd ? 1 : 0);
-    return featureData2({
-        splitLine,
-        refName,
+export function parseNamesFromHeader(header) {
+    const defs = header.split(/\n|\r\n|\r/).filter(Boolean);
+    const defline = defs.at(-1);
+    // Strip the comment marker if there is one, rather than assuming it: a
+    // header kept for tabix with `-S N` instead of `#` is a bare row, and
+    // chopping its first character would rename its first column rather than
+    // fail to find one.
+    return defline?.includes('\t')
+        ? defline
+            .replace(/^#/, '')
+            .split('\t')
+            .map(f => f.trim())
+        : undefined;
+}
+// shared by BedAdapter/BedpeAdapter's getNames(): explicit columnNames config
+// wins, else fall back to parsing the file's own header line
+export async function resolveColumnNames(columnNames, getHeader) {
+    if (columnNames.length) {
+        return columnNames;
+    }
+    return parseNamesFromHeader(await getHeader());
+}
+// A header names the columns but says nothing about their types, so @gmod/bed
+// takes the types from the standard BED columns of the same name — that is what
+// splits `blockSizes` into numbers and leaves an unrecognized column a string.
+// Names win over a configured autoSql, as they did when this file parsed the
+// named case itself.
+export function makeParser({ autoSql, columnNames, }) {
+    return columnNames?.length ? new BED({ columnNames }) : new BED({ autoSql });
+}
+// Decode a BED line's locus (0-based half-open) from its column layout, so the
+// off-by-one rules live in one place instead of being re-derived at each call
+// site. `oneBased` shifts a 1-based-closed start back a base. `hasEndColumn`
+// false (tabix `-b` with no `-e`, e.g. point/GWAS data) means width-1 features.
+// A start/end column collision in a 0-based file is also a point feature (+1).
+export function bedFeatureLocus({ splitLine, colRef, colStart, colEnd, oneBased = false, hasEndColumn = true, }) {
+    const start = +splitLine[colStart] - (oneBased ? 1 : 0);
+    return {
+        refName: splitLine[colRef],
         start,
-        end,
-        parser,
-        uniqueId,
-        scoreColumn,
-        names,
-        disableGeneHeuristic,
-    });
+        end: hasEndColumn
+            ? +splitLine[colEnd] + (colStart === colEnd && !oneBased ? 1 : 0)
+            : start + 1,
+    };
 }
-function parseStrand(strand) {
+// Takes either form: `@gmod/bed`'s parseLine has already run its own
+// parseStrand and hands over ±1/0, while the methylation and bedpe paths read
+// the raw column. `.` and a missing column are unstranded, i.e. 0.
+export function parseStrand(strand) {
     if (strand === '-' || strand === -1) {
         return -1;
     }
@@ -71,24 +99,8 @@ function parseStrand(strand) {
     }
     return 0;
 }
-export function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, disableGeneHeuristic, }) {
-    const data = names
-        ? defaultParser(names, splitLine)
-        : parser.parseLine(splitLine, { uniqueId });
-    const { strand: strand2, score: score2, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
-    const score = scoreColumn ? +data[scoreColumn] : score2 ? +score2 : undefined;
-    const strand = parseStrand(strand2);
-    const subfeatures = rest.blockCount
-        ? makeBlocks({
-            start,
-            uniqueId,
-            refName,
-            chromStarts: rest.chromStarts,
-            blockCount: rest.blockCount,
-            blockSizes: rest.blockSizes,
-            blockStarts: rest.blockStarts,
-        })
-        : undefined;
+export function featureData({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, disableGeneHeuristic, }) {
+    // bedMethyl detection runs on raw splitLine before parsing
     if (isBedMethylFeature({ splitLine, start, end })) {
         return generateBedMethylFeature({
             splitLine,
@@ -98,59 +110,77 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             end,
         });
     }
-    else if (isRepeatMaskerDescriptionField(rest.description)) {
-        const { chromStarts: _4, blockSizes: _5, blockStarts: _6, blockCount: _7, thickStart: _8, thickEnd: _9, description, ...rest2 } = rest;
-        return generateRepeatMaskerFeature({
+    // rastair methylation is identified by its header column names
+    if (names !== undefined && isRastairMethylFeature(names)) {
+        return generateRastairMethylFeature({
+            splitLine,
+            names,
+            uniqueId,
+            refName,
+            start,
+            end,
+        });
+    }
+    const data = parser.parseLine(splitLine, { uniqueId });
+    const { strand: strandRaw, score: scoreRaw, chrom, chromStart, chromEnd, ...rest } = data;
+    const strand = parseStrand(strandRaw);
+    const rawScore = scoreColumn ? data[scoreColumn] : scoreRaw;
+    const score = rawScore === undefined ? undefined : Number(rawScore);
+    const repeat = parseRepeatMaskerDescription(rest.description);
+    if (repeat) {
+        const { description, chromStarts, blockSizes, blockStarts, blockCount, thickStart, thickEnd, ...rest2 } = rest;
+        return {
             ...rest2,
-            description,
+            ...repeat,
             uniqueId,
             score,
             start,
             end,
             strand,
             refName,
-            subfeatures,
-        });
+        };
     }
-    else if (!disableGeneHeuristic &&
-        subfeatures &&
-        isUcscTranscript({
-            strand,
+    const subfeatures = rest.blockCount
+        ? makeBlocks({
+            start,
+            uniqueId,
+            refName,
+            chromStarts: rest.chromStarts,
             blockCount: rest.blockCount,
-            thickStart: rest.thickStart,
-        })) {
+            blockSizes: rest.blockSizes,
+            blockStarts: rest.blockStarts,
+        })
+        : undefined;
+    const transcriptCheck = {
+        strand,
+        blockCount: rest.blockCount,
+        thickStart: rest.thickStart,
+        thickEnd: rest.thickEnd,
+    };
+    if (!disableGeneHeuristic &&
+        subfeatures &&
+        isUcscTranscript(transcriptCheck)) {
         return generateUcscTranscript({
             ...rest,
             score,
             start,
             end,
-            strand,
+            strand: transcriptCheck.strand,
             refName,
             uniqueId,
             subfeatures,
-            thickStart: rest.thickStart,
-            thickEnd: rest.thickEnd,
+            thickStart: transcriptCheck.thickStart,
+            thickEnd: transcriptCheck.thickEnd,
         });
     }
-    else {
-        return {
-            ...rest,
-            uniqueId,
-            score,
-            start,
-            end,
-            strand,
-            refName,
-            subfeatures,
-        };
-    }
-}
-export function arrayify(f) {
-    if (f === undefined) {
-        return undefined;
-    }
-    if (typeof f === 'string') {
-        return f.split(',').map(s => +s);
-    }
-    return f;
+    return {
+        ...rest,
+        uniqueId,
+        score,
+        start,
+        end,
+        strand,
+        refName,
+        subfeatures,
+    };
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "4.3.0",
+  "version": "5.0.0-beta.1",
   "type": "module",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
@@ -21,14 +21,13 @@
     "esm"
   ],
   "dependencies": {
-    "@flatten-js/interval-tree": "^2.0.3",
-    "@gmod/bbi": "^9.0.9",
-    "@gmod/bed": "^2.2.1",
-    "@gmod/tabix": "^3.3.3",
-    "@jbrowse/mobx-state-tree": "^5.6.0",
-    "mobx": "^6.15.3",
+    "@gmod/bbi": "^11.2.3",
+    "@gmod/bed": "^2.3.0",
+    "@gmod/tabix": "^3.8.2",
+    "@jbrowse/mobx-state-tree": "^6.5.1",
+    "mobx": "^7.0.3",
     "rxjs": "^7.8.2",
-    "@jbrowse/core": "^4.3.0"
+    "@jbrowse/core": "^5.0.0-beta.1"
   },
   "publishConfig": {
     "access": "public"
@@ -38,14 +37,11 @@
     "build": "pnpm run /^build:/",
     "test": "cd ../..; jest --passWithNoTests plugins/bed",
     "prebuild": "pnpm clean",
-    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "build:esm": "node ../../node_modules/typescript7/bin/tsc --build tsconfig.build.esm.json",
     "clean": "rimraf esm *.tsbuildinfo"
   },
   "types": "esm/index.d.ts",
   "exports": {
-    ".": {
-      "types": "./esm/index.d.ts",
-      "import": "./esm/index.js"
-    }
+    ".": "./esm/index.js"
   }
 }

package/esm/GuessAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export default function GuessAdapterF(pluginManager: PluginManager): void;

package/esm/GuessAdapter/index.js

@@ -1,71 +0,0 @@
-import { testAdapter } from '@jbrowse/core/util';
-import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
-export default function GuessAdapterF(pluginManager) {
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const fileName = getFileName(file);
-            const indexName = index && getFileName(index);
-            if (testAdapter(fileName, /\.bedpe(\.gz)?$/i, adapterHint, 'BedpeAdapter')) {
-                return {
-                    type: 'BedpeAdapter',
-                    bedpeLocation: file,
-                };
-            }
-            else if (testAdapter(fileName, /\.bb$/i, adapterHint, 'BigBedAdapter') ||
-                testAdapter(fileName, /\.bigbed$/i, adapterHint, 'BigBedAdapter')) {
-                return {
-                    type: 'BigBedAdapter',
-                    bigBedLocation: file,
-                };
-            }
-            else if (testAdapter(fileName, /\.bed$/i, adapterHint, 'BedAdapter')) {
-                return {
-                    type: 'BedAdapter',
-                    bedLocation: file,
-                };
-            }
-            else if (testAdapter(fileName, /\.bg$/i, adapterHint, 'BedGraphAdapter')) {
-                return {
-                    type: 'BedGraphAdapter',
-                    bedGraphLocation: file,
-                };
-            }
-            else if (testAdapter(fileName, /\.bg(\.gz)?$/i, adapterHint, 'BedGraphTabixAdapter')) {
-                return {
-                    type: 'BedGraphTabixAdapter',
-                    bedGraphGzLocation: file,
-                    index: {
-                        location: index || makeIndex(file, '.tbi'),
-                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-                    },
-                };
-            }
-            else if (testAdapter(fileName, /\.bedmethyl\.gz$/i, adapterHint, 'BedTabixAdapter') ||
-                testAdapter(fileName, /\.bed\.gz$/i, adapterHint, 'BedTabixAdapter')) {
-                return {
-                    type: 'BedTabixAdapter',
-                    bedGzLocation: file,
-                    index: {
-                        location: index || makeIndex(file, '.tbi'),
-                        indexType: makeIndexType(indexName, 'CSI', 'TBI'),
-                    },
-                };
-            }
-            else {
-                return adapterGuesser(file, index, adapterHint);
-            }
-        };
-    });
-    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, file));
-    });
-}