@gmod/bed/dist/parser.js

A BED file format parser with autoSql support

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const autoSql_ts_1 = __importDefault(require("./autoSql.js"));
const defaultTypes_ts_1 = __importDefault(require("./defaultTypes.js"));
const util_ts_1 = require("./util.js");
const strandMap = { '.': 0, '-': -1, '+': 1 };
// heuristic that a BED file is BED12 like...the number in col 10 is
// blockCount-like
function isBed12Like(fields) {
    return (fields.length >= 12 &&
        !Number.isNaN(Number.parseInt(fields[9], 10)) &&
        fields[10]?.split(',').filter(f => !!f).length ===
            Number.parseInt(fields[9], 10));
}
class BED {
    constructor(arguments_ = {}) {
        if (arguments_.autoSql) {
            this.autoSql = (0, util_ts_1.detectTypes)(
            // @ts-expect-error
            autoSql_ts_1.default.parse(arguments_.autoSql));
        }
        else if (arguments_.type) {
            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
            if (!defaultTypes_ts_1.default[arguments_.type]) {
                throw new Error('Type not found');
            }
            this.autoSql = (0, util_ts_1.detectTypes)(defaultTypes_ts_1.default[arguments_.type]);
        }
        else {
            this.autoSql = (0, util_ts_1.detectTypes)(defaultTypes_ts_1.default.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');
        let feature = {};
        if (!this.attemptDefaultBed ||
            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
            (this.attemptDefaultBed && isBed12Like(fields))) {
            for (let index = 0; index < autoSql.fields.length; index++) {
                const autoField = autoSql.fields[index];
                let columnValue = fields[index];
                const { isNumeric, isArray, arrayIsNumeric, name } = autoField;
                if (columnValue === null || columnValue === undefined) {
                    break;
                }
                if (columnValue !== '.') {
                    if (isNumeric) {
                        const number_ = Number(columnValue);
                        columnValue = Number.isNaN(number_) ? columnValue : number_;
                    }
                    else if (isArray) {
                        columnValue = columnValue.split(',');
                        if (columnValue.at(-1) === '') {
                            columnValue.pop();
                        }
                        if (arrayIsNumeric) {
                            columnValue = columnValue.map(Number);
                        }
                    }
                    feature[name] = columnValue;
                }
            }
        }
        else {
            const fieldNames = ['chrom', 'chromStart', 'chromEnd', 'name'];
            feature = Object.fromEntries(fields.map((f, index) => [fieldNames[index] || 'field' + index, f]));
            feature.chromStart = +feature.chromStart;
            feature.chromEnd = +feature.chromEnd;
            if (!Number.isNaN(Number.parseFloat(feature.field4))) {
                feature.score = +feature.field4;
                delete feature.field4;
            }
            if (feature.field5 === '+' || feature.field5 === '-') {
                feature.strand = feature.field5;
                delete feature.field5;
            }
        }
        if (uniqueId) {
            feature.uniqueId = uniqueId;
        }
        feature.strand = strandMap[feature.strand] || 0;
        feature.chrom = decodeURIComponent(feature.chrom);
        return feature;
    }
}
exports.default = BED;
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