@jbrowse/core/esm/util/locString.js

JBrowse 2 core libraries used by plugins

const COORD_REGEX = /^(-?\d+)(?:(?:\.\.|[-–])(-?\d+))?(\.\.|[-–])?$/;
const ASSEMBLY_REGEX = /^(?:\{([^}]+)\})?(.+)/;
function parseCoords(suffix, locString) {
    const match = COORD_REGEX.exec(suffix.replaceAll(',', ''));
    if (!match) {
        throw new Error(`could not parse range "${suffix}" on location "${locString}"`);
    }
    const [, startStr, endStr, trailing] = match;
    const start = +startStr;
    return { start, end: endStr ? +endStr : trailing ? undefined : start };
}
export function parseLocStringOneBased(locString, isValidRefName) {
    if (!locString) {
        throw new Error('no location string provided, could not parse');
    }
    let reversed = false;
    if (locString.endsWith('[rev]')) {
        reversed = true;
        locString = locString.slice(0, -5);
    }
    locString = locString.replaceAll(/\s/g, '');
    const assemblyMatch = ASSEMBLY_REGEX.exec(locString);
    if (!assemblyMatch) {
        throw new Error(`invalid location string: "${locString}"`);
    }
    const [, assemblyName, location] = assemblyMatch;
    if (!assemblyName && location.startsWith('{}')) {
        throw new Error(`no assembly name was provided in location "${location}"`);
    }
    const lastColonIdx = location.lastIndexOf(':');
    if (lastColonIdx === -1) {
        if (isValidRefName(location, assemblyName)) {
            return { assemblyName, refName: location, reversed };
        }
        throw new Error(`Unknown feature or sequence "${location}"`);
    }
    const prefix = location.slice(0, lastColonIdx);
    const suffix = location.slice(lastColonIdx + 1);
    const prefixValid = isValidRefName(prefix, assemblyName);
    const locationValid = isValidRefName(location, assemblyName);
    if (prefixValid && locationValid) {
        throw new Error(`ambiguous location string: "${locString}"`);
    }
    if (locationValid) {
        return { assemblyName, refName: location, reversed };
    }
    if (prefixValid) {
        if (!suffix) {
            return { assemblyName, refName: prefix, reversed };
        }
        const coords = parseCoords(suffix, locString);
        return { assemblyName, refName: prefix, reversed, ...coords };
    }
    throw new Error(`unknown reference sequence name in location "${locString}"`);
}
export function parseLocString(locString, isValidRefName) {
    const parsed = parseLocStringOneBased(locString, isValidRefName);
    if (typeof parsed.start === 'number') {
        parsed.start -= 1;
    }
    return parsed;
}