@gmod/bed/esm/parser.js

A BED file format parser with autoSql support

import { parse } from './autoSql.js';
import types from "./defaultTypes.js";
import { detectTypes } from "./util.js";
const strandMap = { '.': 0, '-': -1, '+': 1 };
// Lightweight percent-decode for chrom names: rewrites only well-formed %XX
// escapes and leaves a bare '%' untouched. decodeURIComponent throws on a '%'
// not followed by valid hex (e.g. a contig name like "chr%_test"), taking down
// the whole parse; the BED spec defines chrom as [A-Za-z0-9_] with no
// percent-encoding, so the full UTF-8 machinery isn't warranted here.
function decodeChrom(chrom) {
    return chrom.replace(/%([0-9A-Fa-f]{2})/g, (_, hex) => String.fromCharCode(Number.parseInt(hex, 16)));
}
// heuristic that a BED file is BED12 like...the number in col 10 is
// blockCount-like
function isBed12Like(fields) {
    const blockCount = Number.parseInt(fields[9], 10);
    return (fields.length >= 12 &&
        !Number.isNaN(blockCount) &&
        fields[10]?.split(',').filter(f => f).length === blockCount);
}
export default class BED {
    autoSql;
    attemptDefaultBed;
    constructor(opts = {}) {
        if (opts.autoSql) {
            this.autoSql = detectTypes(parse(opts.autoSql));
        }
        else if (opts.type) {
            if (!types[opts.type]) {
                throw new Error('Type not found');
            }
            this.autoSql = detectTypes(types[opts.type]);
        }
        else {
            this.autoSql = detectTypes(types.defaultBedSchema);
            this.attemptDefaultBed = true;
        }
    }
    /*
     * parses a line of text as a BED line with the loaded autoSql schema
     *
     * @param line - a BED line as tab delimited text or array
     * @param opts - supply opts.uniqueId
     * @return a object representing a feature
     */
    parseLine(line, options = {}) {
        const { autoSql } = this;
        const { uniqueId } = options;
        const fields = Array.isArray(line) ? line : line.split('\t');
        const feature = {};
        if (!this.attemptDefaultBed || isBed12Like(fields)) {
            for (let index = 0; index < autoSql.fields.length; index++) {
                const autoField = autoSql.fields[index];
                const rawColumn = fields[index];
                const { isNumeric, isArray, arrayIsNumeric, name } = autoField;
                if (rawColumn === undefined) {
                    break;
                }
                if (rawColumn !== '.') {
                    if (isNumeric) {
                        const num = Number(rawColumn);
                        feature[name] = Number.isNaN(num) ? rawColumn : num;
                    }
                    else if (isArray) {
                        const parts = rawColumn.split(',');
                        if (parts.at(-1) === '') {
                            parts.pop();
                        }
                        feature[name] = arrayIsNumeric ? parts.map(Number) : parts;
                    }
                    else {
                        feature[name] = rawColumn;
                    }
                }
            }
        }
        else {
            feature.chrom = fields[0];
            feature.chromStart = Number(fields[1]);
            feature.chromEnd = Number(fields[2]);
            if (fields[3] !== undefined) {
                feature.name = fields[3];
            }
            const field4 = fields[4];
            if (field4 !== undefined) {
                const asNum = Number.parseFloat(field4);
                if (Number.isNaN(asNum)) {
                    feature.field4 = field4;
                }
                else {
                    feature.score = asNum;
                }
            }
            const field5 = fields[5];
            if (field5 !== undefined) {
                feature[field5 === '+' || field5 === '-' ? 'strand' : 'field5'] = field5;
            }
            for (let i = 6; i < fields.length; i++) {
                feature['field' + i] = fields[i];
            }
        }
        if (uniqueId) {
            feature.uniqueId = uniqueId;
        }
        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
        feature.strand = strandMap[feature.strand] ?? 0;
        feature.chrom = decodeChrom(String(feature.chrom));
        return feature;
    }
}
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