@jbrowse/plugin-bed 3.7.0 → 4.0.1

package/esm/generateUcscTranscript.js

@@ -1,13 +1,29 @@
 export function isUcscTranscript({ thickStart, blockCount, strand, }) {
     return thickStart && blockCount && strand !== 0;
 }
+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);
+        cumulativeWidth += cds.end - cds.start;
+    }
+    return phaseMap;
+}
+function frameToPhase(frame) {
+    return (3 - frame) % 3;
+}
 export function generateUcscTranscript(data) {
-    const { strand = 0, chrom: _1, chromStart: _2, chromEnd: _3, chromStarts, blockStarts, blockSizes, uniqueId, ...rest } = data;
-    const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, refName, ...rest2 } = rest;
-    const subfeatures = [];
+    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 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;
     if (cdsStartStat === 'none' && cdsEndStat === 'none') {
         return {
@@ -16,97 +32,62 @@ export function generateUcscTranscript(data) {
             strand,
             type: 'transcript',
             refName,
-            subfeatures: feats.map(e => ({
-                ...e,
-                type: 'exon',
-            })),
+            start,
+            end,
+            subfeatures: feats.map(e => ({ ...e, type: 'exon' })),
         };
     }
-    else {
+    let calculatedPhases;
+    if (!exonFrames) {
+        const cdsRegions = [];
         for (const block of feats) {
-            const start = block.start;
-            const end = block.end;
-            if (thickStart >= end) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                    start,
-                    end,
-                    refName,
-                });
-            }
-            else if (thickStart > start && thickStart < end && thickEnd >= end) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                    start,
-                    end: thickStart,
-                    refName,
-                }, {
-                    type: 'CDS',
-                    phase: 0,
-                    start: thickStart,
-                    end,
-                    refName,
+            const { start, end } = block;
+            if (thickStart < end && thickEnd > start) {
+                cdsRegions.push({
+                    start: Math.max(start, thickStart),
+                    end: Math.min(end, thickEnd),
                 });
             }
-            else if (thickStart <= start && thickEnd >= end) {
-                subfeatures.push({
-                    type: 'CDS',
-                    phase: 0,
-                    start,
-                    end,
-                    refName,
-                });
+        }
+        calculatedPhases = calculatePhasesFromCds(cdsRegions, strand);
+    }
+    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 });
+        }
+        else if (thickEnd <= start) {
+            subfeatures.push({ type: threeUTR, start, end, refName });
+        }
+        else {
+            if (start < thickStart) {
+                subfeatures.push({ type: fiveUTR, start, end: thickStart, refName });
             }
-            else if (thickStart > start && thickStart < end && thickEnd < end) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'five' : 'three'}_prime_UTR`,
-                    start,
-                    end: thickStart,
-                    refName,
-                }, {
-                    type: 'CDS',
-                    phase: 0,
-                    start: thickStart,
-                    end: thickEnd,
-                    refName,
-                }, {
-                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                    start: thickEnd,
-                    end,
-                    refName,
-                });
+            const cdsStart = Math.max(start, thickStart);
+            const cdsEnd = Math.min(end, thickEnd);
+            let phase = 0;
+            if (exonFrames) {
+                const frame = exonFrames[i];
+                if (frame !== undefined && frame >= 0) {
+                    phase = frameToPhase(frame);
+                }
             }
-            else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-                subfeatures.push({
-                    type: 'CDS',
-                    phase: 0,
-                    start,
-                    end: thickEnd,
-                    refName,
-                }, {
-                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                    start: thickEnd,
-                    end,
-                    refName,
-                });
+            else if (calculatedPhases) {
+                phase = calculatedPhases.get(cdsStart) ?? 0;
             }
-            else if (thickEnd <= start) {
-                subfeatures.push({
-                    type: `${strand > 0 ? 'three' : 'five'}_prime_UTR`,
-                    start,
-                    end,
-                    refName,
-                });
+            subfeatures.push({
+                type: 'CDS',
+                phase,
+                start: cdsStart,
+                end: cdsEnd,
+                refName,
+            });
+            if (end > thickEnd) {
+                subfeatures.push({ type: threeUTR, start: thickEnd, end, refName });
             }
         }
-        return {
-            ...rest2,
-            uniqueId,
-            strand,
-            type: 'mRNA',
-            refName,
-            subfeatures,
-        };
     }
     return {
         ...rest2,
@@ -114,6 +95,8 @@ export function generateUcscTranscript(data) {
         strand,
         type: 'mRNA',
         refName,
+        start,
+        end,
         subfeatures,
     };
 }

package/esm/index.js

@@ -1,16 +1,13 @@
 import Plugin from '@jbrowse/core/Plugin';
-import BedAdapterF from './BedAdapter';
-import BedGraphAdapterF from './BedGraphAdapter';
-import BedGraphTabixAdapterF from './BedGraphTabixAdapter';
-import BedTabixAdapterF from './BedTabixAdapter';
-import BedpeAdapterF from './BedpeAdapter';
-import BigBedAdapterF from './BigBedAdapter';
-import GuessAdapterF from './GuessAdapter';
+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";
 export default class BedPlugin extends Plugin {
-    constructor() {
-        super(...arguments);
-        this.name = 'BedPlugin';
-    }
+    name = 'BedPlugin';
     install(pluginManager) {
         BigBedAdapterF(pluginManager);
         BedAdapterF(pluginManager);

package/esm/types.d.ts

@@ -3,16 +3,7 @@ export interface MinimalFeature {
     start: number;
     end: number;
     refName: string;
+    uniqueId?: string;
+    phase?: number;
     [key: string]: unknown;
 }
-export interface TranscriptFeat extends MinimalFeature {
-    uniqueId: string;
-    thickStart: number;
-    thickEnd: number;
-    blockCount: number;
-    blockSizes: number[];
-    chromStarts: number[];
-    refName: string;
-    strand?: number;
-    subfeatures: MinimalFeature[];
-}

package/esm/util.d.ts

@@ -1,3 +1,4 @@
+import type { MinimalFeature } from './types';
 import type BED from '@gmod/bed';
 export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
     blockCount: number;
@@ -23,95 +24,18 @@ export declare function featureData({ line, colRef, colStart, colEnd, scoreColum
     parser: BED;
     uniqueId: string;
     names?: string[];
-}): {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    code: string | undefined;
-    score: number;
-    strand: string | undefined;
-    color: string | undefined;
-    source: string | undefined;
-    n_valid_cov: string | undefined;
-    fraction_modified: string | undefined;
-    n_mod: string | undefined;
-    n_canonical: string | undefined;
-    n_other_mod: string | undefined;
-    n_delete: string | undefined;
-    n_fail: string | undefined;
-    n_diff: string | undefined;
-    n_nocall: string | undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    bitsw_score: string | undefined;
-    percent_div: string | undefined;
-    percent_del: string | undefined;
-    percent_ins: string | undefined;
-    query_chr: string | undefined;
-    query_begin: string | undefined;
-    query_end: string | undefined;
-    query_remaining: string | undefined;
-    orientation: string | undefined;
-    matching_repeat_name: string | undefined;
-    matching_repeat_class: string | undefined;
-    matching_repeat_begin: string | undefined;
-    matching_repeat_end: string | undefined;
-    matching_repeat_remaining: string | undefined;
-    repeat_id: string | undefined;
-    description?: undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    description: undefined;
-    bitsw_score?: undefined;
-    percent_div?: undefined;
-    percent_del?: undefined;
-    percent_ins?: undefined;
-    query_chr?: undefined;
-    query_begin?: undefined;
-    query_end?: undefined;
-    query_remaining?: undefined;
-    orientation?: undefined;
-    matching_repeat_name?: undefined;
-    matching_repeat_class?: undefined;
-    matching_repeat_begin?: undefined;
-    matching_repeat_end?: undefined;
-    matching_repeat_remaining?: undefined;
-    repeat_id?: undefined;
-} | {
+}): FeatureData;
+interface FeatureData {
     uniqueId: string;
-    strand: number;
-    type: string;
     refName: string;
-    subfeatures: {
-        type: string;
-        start: number;
-        end: number;
-        refName: string;
-    }[];
-    start: number;
-    end: number;
-} | {
-    uniqueId: string;
-    score: number | undefined;
     start: number;
     end: number;
-    strand: any;
-    refName: string;
-    subfeatures: {
-        uniqueId: string;
-        start: number;
-        end: number;
-        refName: string;
-        type: string;
-    }[] | undefined;
-};
+    strand?: number | string;
+    score?: number;
+    type?: string;
+    subfeatures?: MinimalFeature[];
+    [key: string]: unknown;
+}
 export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
     splitLine: string[];
     refName: string;
@@ -121,93 +45,6 @@ export declare function featureData2({ splitLine, refName, start, end, parser, u
     uniqueId: string;
     scoreColumn: string;
     names?: string[];
-}): {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    code: string | undefined;
-    score: number;
-    strand: string | undefined;
-    color: string | undefined;
-    source: string | undefined;
-    n_valid_cov: string | undefined;
-    fraction_modified: string | undefined;
-    n_mod: string | undefined;
-    n_canonical: string | undefined;
-    n_other_mod: string | undefined;
-    n_delete: string | undefined;
-    n_fail: string | undefined;
-    n_diff: string | undefined;
-    n_nocall: string | undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    bitsw_score: string | undefined;
-    percent_div: string | undefined;
-    percent_del: string | undefined;
-    percent_ins: string | undefined;
-    query_chr: string | undefined;
-    query_begin: string | undefined;
-    query_end: string | undefined;
-    query_remaining: string | undefined;
-    orientation: string | undefined;
-    matching_repeat_name: string | undefined;
-    matching_repeat_class: string | undefined;
-    matching_repeat_begin: string | undefined;
-    matching_repeat_end: string | undefined;
-    matching_repeat_remaining: string | undefined;
-    repeat_id: string | undefined;
-    description?: undefined;
-} | {
-    uniqueId: string;
-    refName: string;
-    start: number;
-    end: number;
-    description: undefined;
-    bitsw_score?: undefined;
-    percent_div?: undefined;
-    percent_del?: undefined;
-    percent_ins?: undefined;
-    query_chr?: undefined;
-    query_begin?: undefined;
-    query_end?: undefined;
-    query_remaining?: undefined;
-    orientation?: undefined;
-    matching_repeat_name?: undefined;
-    matching_repeat_class?: undefined;
-    matching_repeat_begin?: undefined;
-    matching_repeat_end?: undefined;
-    matching_repeat_remaining?: undefined;
-    repeat_id?: undefined;
-} | {
-    uniqueId: string;
-    strand: number;
-    type: string;
-    refName: string;
-    subfeatures: {
-        type: string;
-        start: number;
-        end: number;
-        refName: string;
-    }[];
-    start: number;
-    end: number;
-} | {
-    uniqueId: string;
-    score: number | undefined;
-    start: number;
-    end: number;
-    strand: any;
-    refName: string;
-    subfeatures: {
-        uniqueId: string;
-        start: number;
-        end: number;
-        refName: string;
-        type: string;
-    }[] | undefined;
-};
+}): FeatureData;
 export declare function arrayify(f?: string | number[]): number[] | undefined;
+export {};

package/esm/util.js

@@ -1,16 +1,18 @@
-import { generateBedMethylFeature, isBedMethylFeature, } from './generateBedMethylFeature';
-import { generateRepeatMaskerFeature, isRepeatMaskerDescriptionField, } from './generateRepeatMaskerFeature';
-import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript';
+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;
-    const r = [];
-    for (let i = 0; i < splitLine.length; i++) {
-        if (fields[i] === 'blockCount') {
-            hasBlockCount = true;
+    for (const [i, element] of splitLine.entries()) {
+        const field = fields[i];
+        if (field) {
+            obj[field] = element;
+            if (field === 'blockCount') {
+                hasBlockCount = true;
+            }
         }
-        r.push([fields[i], splitLine[i]]);
     }
-    const obj = Object.fromEntries(r);
     if (hasBlockCount) {
         const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
         return {
@@ -23,22 +25,19 @@ function defaultParser(fields, splitLine) {
             blockCount: blockCount ? +blockCount : undefined,
         };
     }
-    else {
-        return obj;
-    }
+    return obj;
 }
 export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
     const subfeatures = [];
-    const starts = chromStarts || blockStarts || [];
+    const starts = chromStarts ?? blockStarts ?? [];
     for (let b = 0; b < blockCount; b++) {
-        const bmin = (starts[b] || 0) + start;
-        const bsize = blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b];
+        const bmin = (starts[b] ?? 0) + start;
+        const bsize = blockSizes?.[b];
         if (bsize && bsize > 0) {
-            const bmax = bmin + bsize;
             subfeatures.push({
                 uniqueId: `${uniqueId}-${b}`,
                 start: bmin,
-                end: bmax,
+                end: bmin + bsize,
                 refName,
                 type: 'block',
             });
@@ -62,13 +61,22 @@ export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parse
         names,
     });
 }
+function parseStrand(strand) {
+    if (strand === '-' || strand === -1) {
+        return -1;
+    }
+    if (strand === '+' || strand === 1) {
+        return 1;
+    }
+    return 0;
+}
 export function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
     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 = typeof strand2 === 'string' ? (strand2 === '-' ? -1 : 1) : strand2;
+    const strand = parseStrand(strand2);
     const subfeatures = rest.blockCount
         ? makeBlocks({
             start,
@@ -89,13 +97,12 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             end,
         });
     }
-    else if (isRepeatMaskerDescriptionField(rest.description)) {
-        const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
+    if (isRepeatMaskerDescriptionField(rest.description)) {
+        const { chromStarts: _4, blockSizes: _5, blockStarts: _6, blockCount: _7, thickStart: _8, thickEnd: _9, description, ...rest2 } = rest;
         return generateRepeatMaskerFeature({
             ...rest2,
-            uniqueId,
             description,
-            type,
+            uniqueId,
             score,
             start,
             end,
@@ -104,22 +111,14 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             subfeatures,
         });
     }
-    else if (subfeatures &&
+    if (subfeatures &&
         isUcscTranscript({
             strand,
             blockCount: rest.blockCount,
             thickStart: rest.thickStart,
         })) {
-        const { chromStarts, blockSizes, type, blockCount, thickStart, thickEnd, description, } = rest;
         return generateUcscTranscript({
             ...rest,
-            description,
-            chromStarts,
-            thickStart,
-            thickEnd,
-            blockSizes,
-            blockCount,
-            type,
             score,
             start,
             end,
@@ -127,25 +126,27 @@ export function featureData2({ splitLine, refName, start, end, parser, uniqueId,
             refName,
             uniqueId,
             subfeatures,
+            thickStart: rest.thickStart,
+            thickEnd: rest.thickEnd,
         });
     }
-    else {
-        return {
-            ...rest,
-            uniqueId,
-            score,
-            start,
-            end,
-            strand,
-            refName,
-            subfeatures,
-        };
-    }
+    return {
+        ...rest,
+        uniqueId,
+        score,
+        start,
+        end,
+        strand,
+        refName,
+        subfeatures,
+    };
 }
 export function arrayify(f) {
-    return f !== undefined
-        ? typeof f === 'string'
-            ? f.split(',').map(f => +f)
-            : f
-        : undefined;
+    if (f === undefined) {
+        return undefined;
+    }
+    if (typeof f === 'string') {
+        return f.split(',').map(s => +s);
+    }
+    return f;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "3.7.0",
+  "version": "4.0.1",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -15,43 +15,36 @@
     "directory": "plugins/bed"
   },
   "author": "JBrowse Team",
-  "distMain": "dist/index.js",
-  "srcMain": "src/index.ts",
-  "main": "dist/index.js",
+  "main": "esm/index.js",
   "files": [
-    "dist",
     "esm"
   ],
-  "scripts": {
-    "build": "npm-run-all build:*",
-    "test": "cd ../..; jest --passWithNoTests plugins/bed",
-    "prepublishOnly": "yarn test",
-    "prepack": "yarn build && yarn useDist",
-    "postpack": "yarn useSrc",
-    "useDist": "node ../../scripts/useDist.js",
-    "useSrc": "node ../../scripts/useSrc.js",
-    "prebuild": "npm run clean",
-    "build:esm": "tsc --build tsconfig.build.esm.json",
-    "build:commonjs": "tsc --build tsconfig.build.commonjs.json",
-    "clean": "rimraf dist esm *.tsbuildinfo"
-  },
   "dependencies": {
-    "@flatten-js/interval-tree": "^2.0.0",
-    "@gmod/bbi": "^7.0.0",
-    "@gmod/bed": "^2.1.2",
-    "@gmod/bgzf-filehandle": "^4.0.0",
-    "@gmod/tabix": "^3.0.1",
-    "@jbrowse/core": "^3.7.0",
-    "mobx": "^6.0.0",
-    "mobx-react": "^9.0.0",
-    "mobx-state-tree": "^5.0.0",
-    "rxjs": "^7.0.0"
+    "@flatten-js/interval-tree": "^2.0.3",
+    "@gmod/bbi": "^8.1.1",
+    "@gmod/bed": "^2.1.7",
+    "@gmod/tabix": "^3.2.2",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "mobx": "^6.15.0",
+    "rxjs": "^7.8.2",
+    "@jbrowse/core": "^4.0.1"
   },
   "publishConfig": {
     "access": "public"
   },
-  "distModule": "esm/index.js",
-  "srcModule": "src/index.ts",
-  "module": "esm/index.js",
-  "gitHead": "85bdd0d58286b7adbfd408146b15847676317635"
-}
+  "sideEffects": false,
+  "scripts": {
+    "build": "pnpm run /^build:/",
+    "test": "cd ../..; jest --passWithNoTests plugins/bed",
+    "prebuild": "pnpm clean",
+    "build:esm": "tsc -p tsconfig.build.esm.json",
+    "clean": "rimraf esm *.tsbuildinfo"
+  },
+  "types": "esm/index.d.ts",
+  "exports": {
+    ".": {
+      "types": "./esm/index.d.ts",
+      "import": "./esm/index.js"
+    }
+  }
+}