@jbrowse/plugin-bed 3.7.0 → 4.0.0

package/dist/util.js

@@ -1,157 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeBlocks = makeBlocks;
-exports.featureData = featureData;
-exports.featureData2 = featureData2;
-exports.arrayify = arrayify;
-const generateBedMethylFeature_1 = require("./generateBedMethylFeature");
-const generateRepeatMaskerFeature_1 = require("./generateRepeatMaskerFeature");
-const generateUcscTranscript_1 = require("./generateUcscTranscript");
-function defaultParser(fields, splitLine) {
-    let hasBlockCount = false;
-    const r = [];
-    for (let i = 0; i < splitLine.length; i++) {
-        if (fields[i] === '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 {
-            ...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;
-    }
-}
-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 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;
-}
-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,
-    });
-}
-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 subfeatures = rest.blockCount
-        ? makeBlocks({
-            start,
-            uniqueId,
-            refName,
-            chromStarts: rest.chromStarts,
-            blockCount: rest.blockCount,
-            blockSizes: rest.blockSizes,
-            blockStarts: rest.blockStarts,
-        })
-        : undefined;
-    if ((0, generateBedMethylFeature_1.isBedMethylFeature)({ splitLine, start, end })) {
-        return (0, generateBedMethylFeature_1.generateBedMethylFeature)({
-            splitLine,
-            uniqueId,
-            refName,
-            start,
-            end,
-        });
-    }
-    else if ((0, generateRepeatMaskerFeature_1.isRepeatMaskerDescriptionField)(rest.description)) {
-        const { chromStarts, blockSizes, blockStarts, type, blockCount, thickStart, thickEnd, description, ...rest2 } = rest;
-        return (0, generateRepeatMaskerFeature_1.generateRepeatMaskerFeature)({
-            ...rest2,
-            uniqueId,
-            description,
-            type,
-            score,
-            start,
-            end,
-            strand,
-            refName,
-            subfeatures,
-        });
-    }
-    else if (subfeatures &&
-        (0, generateUcscTranscript_1.isUcscTranscript)({
-            strand,
-            blockCount: rest.blockCount,
-            thickStart: rest.thickStart,
-        })) {
-        const { chromStarts, blockSizes, type, blockCount, thickStart, thickEnd, description, } = rest;
-        return (0, generateUcscTranscript_1.generateUcscTranscript)({
-            ...rest,
-            description,
-            chromStarts,
-            thickStart,
-            thickEnd,
-            blockSizes,
-            blockCount,
-            type,
-            score,
-            start,
-            end,
-            strand,
-            refName,
-            uniqueId,
-            subfeatures,
-        });
-    }
-    else {
-        return {
-            ...rest,
-            uniqueId,
-            score,
-            start,
-            end,
-            strand,
-            refName,
-            subfeatures,
-        };
-    }
-}
-function arrayify(f) {
-    return f !== undefined
-        ? typeof f === 'string'
-            ? f.split(',').map(f => +f)
-            : f
-        : undefined;
-}