@gmod/cram/esm/cramFile/codecs/byteArrayStop.js

read CRAM files with pure Javascript

import CramCodec from "./_base.js";
import { CramMalformedError } from "../../errors.js";
import { CramBufferOverrunError } from "./getBits.js";
export default class ByteArrayStopCodec extends CramCodec {
    decode(_slice, _coreDataBlock, blocksByContentId, cursors) {
        const { blockContentId } = this.parameters;
        const contentBlock = blocksByContentId[blockContentId];
        if (!contentBlock) {
            throw new CramMalformedError(`no block found with content ID ${blockContentId}`);
        }
        const cursor = cursors.externalBlocks.getCursor(blockContentId);
        return this._decodeByteArray(contentBlock, cursor);
    }
    _decodeByteArray(contentBlock, cursor) {
        const dataBuffer = contentBlock.content;
        const { stopByte } = this.parameters;
        // scan to the next stop byte
        const startPosition = cursor.bytePosition;
        let stopPosition = cursor.bytePosition;
        while (dataBuffer[stopPosition] !== stopByte &&
            stopPosition < dataBuffer.length) {
            if (stopPosition === dataBuffer.length) {
                throw new CramBufferOverrunError('byteArrayStop reading beyond length of data buffer?');
            }
            stopPosition = stopPosition + 1;
        }
        cursor.bytePosition = stopPosition + 1;
        return dataBuffer.subarray(startPosition, stopPosition);
    }
}
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