bgzLineReader.js

import {buildOptions} from "../util/igvUtils.js"
import {BGZip, igvxhr} from "../../node_modules/igv-utils/src/index.js"

/**
 * Class to iterate line-by-line over a BGZipped text file.  This class is useful for iterating from the start of
 * the file.  Not useful for indexed queries.
 */

class BGZLineReader {

    constructor(config) {
        this.config = config
        this.filePtr = 0
        this.bufferPtr = 0
        this.buffer
    }

    async nextLine() {

        let result = undefined

        try {
            while (true) {
                const length = this.buffer ? this.buffer.length : 0
                while (this.bufferPtr < length) {
                    const c = String.fromCharCode(this.buffer[this.bufferPtr++])
                    if (c === '\r') continue
                    if (c === '\n') {
                        return result
                    }
                    result = result ? result + c : c
                }
                if (this.eof) {
                    return result
                } else {
                    await this.readNextBlock()
                }
            }
        } catch (e) {
            console.warn(e)
            this.eof = true
            return result
        }
    }

    async readNextBlock() {

        const bsizeOptions = buildOptions(this.config, {
            range: {
                start: this.filePtr,
                size: 26
            }
        })
        const abuffer = await igvxhr.loadArrayBuffer(this.config.url, bsizeOptions)
        const bufferSize = BGZip.bgzBlockSize(abuffer)
        //console.log(`next block ${this.filePtr}  ${bufferSize}`);

        if (bufferSize === 0) {
            this.eof = true
            this.buffer = undefined
        } else {

            const options = buildOptions(this.config, {range: {start: this.filePtr, size: bufferSize}})
            const data = await igvxhr.loadArrayBuffer(this.config.url, options)
            if (data.byteLength < bufferSize) {
                this.eof = true // Assumption
            }
            this.buffer = BGZip.unbgzf(data)
            this.bufferPtr = 0
            this.filePtr += data.byteLength //data.byteLength;
        }
    }

}

export default BGZLineReader