/**

* BAM file reader using @gmod/bam for browser-based access.

* Supports remote URLs and local File objects.

*/

import { BamFile } from '@gmod/bam';

import { RemoteFile, LocalFile } from 'generic-filehandle';

export class BamReader {

/**

* Create a BamReader instance.

*

* @param {Object} config

* @param {string} [config.url] - URL to BAM file (for remote access)

* @param {string} [config.indexUrl] - URL to BAI index file

* @param {File} [config.bamFile] - Local File object (for file input)

* @param {File} [config.indexFile] - Local BAI File object

* @param {string} [config.label] - Display name for this sample

*/

constructor(config) {

this.label = config.label || '';

const bamOpts = {};

if (config.url) {

bamOpts.bamFilehandle = new RemoteFile(config.url);

bamOpts.baiFilehandle = new RemoteFile(

config.indexUrl || config.url + '.bai',

);

} else if (config.bamFile) {

bamOpts.bamFilehandle = new LocalFile(config.bamFile);

bamOpts.baiFilehandle = new LocalFile(config.indexFile);

}

this.bam = new BamFile(bamOpts);

this._headerPromise = null;

}

/**

* Get the BAM header (cached).

*

* @returns {Promise<string>}

*/

async getHeader() {

if (!this._headerPromise) {

this._headerPromise = this.bam.getHeader();

}

return this._headerPromise;

}

/**

* Fetch reads from a genomic region.

*

* @param {string} chrom - Chromosome name

* @param {number} start - Start position (0-based)

* @param {number} end - End position

* @returns {Promise<Array>} Array of BAM records

*/

async fetchReads(chrom, start, end) {

// Ensure header is loaded first

await this.getHeader();

const records = await this.bam.getRecordsForRange(chrom, start, end);

return records;

}

}