@jbrowse/plugin-bed 2.16.1 → 2.18.0

package/esm/util.d.ts

@@ -1,48 +1,203 @@
-import BED from '@gmod/bed';
-import { SimpleFeature } from '@jbrowse/core/util';
-export interface MinimalFeature {
+import type BED from '@gmod/bed';
+export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
+    blockCount: number;
+    start: number;
+    uniqueId: string;
+    refName: string;
+    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, }: {
+    line: string;
+    colRef: number;
+    colStart: number;
+    colEnd: number;
+    scoreColumn: string;
+    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;
-    [key: string]: unknown;
-}
-export interface TranscriptFeat extends MinimalFeature {
-    thickStart: number;
-    thickEnd: number;
-    blockCount: number;
-    blockSizes: number[];
-    chromStarts: number[];
+    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;
-    strand?: number;
-    subfeatures: MinimalFeature[];
-}
-export declare function ucscProcessedTranscript(feature: TranscriptFeat): TranscriptFeat | {
+    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: MinimalFeature[];
+    subfeatures: import("./types").MinimalFeature[];
+    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;
 };
-export declare function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }: {
-    blockCount: number;
+export declare function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }: {
+    splitLine: string[];
+    refName: string;
     start: number;
+    end: number;
+    parser: BED;
     uniqueId: string;
-    refName: string;
-    chromStarts?: number[];
-    blockSizes: number[];
-    blockStarts?: number[];
+    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;
-}[];
-export declare function featureData(line: string, colRef: number, colStart: number, colEnd: number, scoreColumn: string, parser: BED, uniqueId: string, names?: string[]): SimpleFeature;
-export declare function isUcscProcessedTranscript(f: {
-    thickStart?: number;
-    blockCount?: number;
-    strand?: number;
-}): boolean | 0 | undefined;
+    refName: string;
+    subfeatures: import("./types").MinimalFeature[];
+    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;
+};
+export declare function arrayify(f?: string | number[]): number[] | undefined;

package/esm/util.js

@@ -1,173 +1,151 @@
-import { SimpleFeature } from '@jbrowse/core/util';
-export function ucscProcessedTranscript(feature) {
-    const { subfeatures: oldSubfeatures, thickStart, thickEnd, blockCount, blockSizes, chromStarts, refName, strand = 0, ...rest } = feature;
-    if (!thickStart || !thickEnd || !strand) {
-        return feature;
-    }
-    const subfeatures = [];
-    oldSubfeatures
-        .filter(child => child.type === 'block')
-        .sort((a, b) => a.start - b.start)
-        .forEach(block => {
-        const start = block.start;
-        const end = block.end;
-        if (thickStart >= end) {
-            // left-side UTR
-            const prime = strand > 0 ? 'five' : 'three';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd >= end) {
-            // UTR | CDS
-            const prime = strand > 0 ? 'five' : 'three';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                start: thickStart,
-                end,
-                refName,
-            });
+import { generateBedMethylFeature, isBedMethylFeature, } from './generateBedMethylFeature';
+import { generateRepeatMaskerFeature, isRepeatMaskerDescriptionField, } from './generateRepeatMaskerFeature';
+import { generateUcscTranscript, isUcscTranscript, } from './generateUcscTranscript';
+function defaultParser(fields, splitLine) {
+    let hasBlockCount = false;
+    const r = [];
+    for (let i = 0; i < splitLine.length; i++) {
+        if (fields[i] === 'blockCount') {
+            hasBlockCount = true;
         }
-        else if (thickStart <= start && thickEnd >= end) {
-            // CDS
-            subfeatures.push({
-                type: 'CDS',
-                start,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart > start && thickStart < end && thickEnd < end) {
-            // UTR | CDS | UTR
-            const leftPrime = strand > 0 ? 'five' : 'three';
-            const rightPrime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: `${leftPrime}_prime_UTR`,
-                start,
-                end: thickStart,
-                refName,
-            }, {
-                type: 'CDS',
-                start: thickStart,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${rightPrime}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickStart <= start && thickEnd > start && thickEnd < end) {
-            // CDS | UTR
-            const prime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: 'CDS',
-                start,
-                end: thickEnd,
-                refName,
-            }, {
-                type: `${prime}_prime_UTR`,
-                start: thickEnd,
-                end,
-                refName,
-            });
-        }
-        else if (thickEnd <= start) {
-            // right-side UTR
-            const prime = strand > 0 ? 'three' : 'five';
-            subfeatures.push({
-                type: `${prime}_prime_UTR`,
-                start,
-                end,
-                refName,
-            });
-        }
-    });
-    return { ...rest, strand, type: 'mRNA', refName, subfeatures };
-}
-function defaultParser(fields, line) {
-    const obj = Object.fromEntries(line.split('\t').map((f, i) => [fields[i], f]));
-    const { blockStarts, blockCount, chromStarts, thickEnd, thickStart, blockSizes, ...rest } = obj;
-    return {
-        ...rest,
-        blockStarts: blockStarts === null || blockStarts === void 0 ? void 0 : blockStarts.split(',').map(r => +r),
-        chromStarts: chromStarts === null || chromStarts === void 0 ? void 0 : chromStarts.split(',').map(r => +r),
-        blockSizes: blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes.split(',').map(r => +r),
-        thickStart: thickStart ? +thickStart : undefined,
-        thickEnd: thickEnd ? +thickEnd : undefined,
-        blockCount: blockCount ? +blockCount : undefined,
-    };
+        r.push([fields[i], splitLine[i]]);
+    }
+    const obj = Object.fromEntries(r);
+    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,
+        };
+    }
+    else {
+        return obj;
+    }
 }
 export function makeBlocks({ start, uniqueId, refName, chromStarts, blockCount, blockSizes, blockStarts, }) {
     const subfeatures = [];
     const starts = chromStarts || blockStarts || [];
     for (let b = 0; b < blockCount; b++) {
         const bmin = (starts[b] || 0) + start;
-        const bmax = bmin + (blockSizes[b] || 0);
-        subfeatures.push({
-            uniqueId: `${uniqueId}-${b}`,
-            start: bmin,
-            end: bmax,
-            refName,
-            type: 'block',
-        });
+        const bsize = blockSizes === null || blockSizes === void 0 ? void 0 : blockSizes[b];
+        if (bsize && bsize > 0) {
+            const bmax = bmin + bsize;
+            subfeatures.push({
+                uniqueId: `${uniqueId}-${b}`,
+                start: bmin,
+                end: bmax,
+                refName,
+                type: 'block',
+            });
+        }
     }
     return subfeatures;
 }
-export function featureData(line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names) {
-    const l = line.split('\t');
-    const refName = l[colRef];
-    const start = +l[colStart];
-    const colSame = colStart === colEnd ? 1 : 0;
-    const end = +l[colEnd] + colSame;
+export function featureData({ line, colRef, colStart, colEnd, scoreColumn, parser, uniqueId, names, }) {
+    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,
+        start,
+        end,
+        parser,
+        uniqueId,
+        scoreColumn,
+        names,
+    });
+}
+export function featureData2({ splitLine, refName, start, end, parser, uniqueId, scoreColumn, names, }) {
     const data = names
-        ? defaultParser(names, line)
-        : parser.parseLine(line, { uniqueId });
-    const { blockCount, blockSizes, blockStarts, chromStarts, thickStart, thickEnd, type, score, chrom: _1, chromStart: _2, chromEnd: _3, ...rest } = data;
-    const subfeatures = blockCount
+        ? 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 subfeatures = rest.blockCount
         ? makeBlocks({
             start,
             uniqueId,
             refName,
+            chromStarts: rest.chromStarts,
+            blockCount: rest.blockCount,
+            blockSizes: rest.blockSizes,
+            blockStarts: rest.blockStarts,
+        })
+        : undefined;
+    if (isBedMethylFeature({ splitLine, start, end })) {
+        return generateBedMethylFeature({
+            splitLine,
+            uniqueId,
+            refName,
+            start,
+            end,
+        });
+    }
+    else if (isRepeatMaskerDescriptionField(rest.description)) {
+        const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
+        return generateRepeatMaskerFeature({
+            ...rest2,
+            uniqueId,
+            description,
+            type,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            subfeatures,
+        });
+    }
+    else if (subfeatures &&
+        isUcscTranscript({
+            strand,
+            blockCount: rest.blockCount,
+            thickStart: rest.thickStart,
+        })) {
+        const { chromStarts, blockSizes, type, blockCount, thickStart, thickEnd, description, } = rest;
+        return generateUcscTranscript({
+            ...rest,
+            description,
             chromStarts,
-            blockCount,
+            thickStart,
+            thickEnd,
             blockSizes,
-            blockStarts,
-        })
-        : [];
-    const f = {
-        ...rest,
-        type,
-        score: scoreColumn ? +data[scoreColumn] : score,
-        start,
-        end,
-        refName,
-        uniqueId,
-        subfeatures,
-    };
-    return new SimpleFeature({
-        id: uniqueId,
-        data: isUcscProcessedTranscript(data)
-            ? ucscProcessedTranscript({
-                thickStart: thickStart,
-                thickEnd: thickEnd,
-                blockCount: blockCount,
-                blockSizes: blockSizes,
-                chromStarts: chromStarts,
-                ...f,
-            })
-            : f,
-    });
+            blockCount,
+            type,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            uniqueId,
+            subfeatures,
+        });
+    }
+    else {
+        return {
+            ...rest,
+            uniqueId,
+            score,
+            start,
+            end,
+            strand,
+            refName,
+            subfeatures,
+        };
+    }
 }
-export function isUcscProcessedTranscript(f) {
-    return f.thickStart && f.blockCount && f.strand !== 0;
+export function arrayify(f) {
+    return f !== undefined
+        ? typeof f === 'string'
+            ? f.split(',').map(f => +f)
+            : f
+        : undefined;
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-bed",
-  "version": "2.16.1",
+  "version": "2.18.0",
   "description": "JBrowse 2 bed adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -55,5 +55,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "c6a658d2344989895543f0456b1cf7dd3b937769"
+  "gitHead": "c344ea60099cb7e460b77f15808946b24a7eee74"
 }