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

read CRAM files with pure Javascript

"use strict";
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const _base_ts_1 = __importDefault(require("./_base.js"));
const errors_ts_1 = require("../../errors.js");
class ByteArrayStopCodec extends _base_ts_1.default {
    decode(_slice, _coreDataBlock, blocksByContentId, cursors) {
        const { blockContentId } = this.parameters;
        const contentBlock = blocksByContentId[blockContentId];
        if (!contentBlock) {
            throw new errors_ts_1.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;
        const startPosition = cursor.bytePosition;
        const len = dataBuffer.length;
        let stopPosition = startPosition;
        while (stopPosition < len && dataBuffer[stopPosition] !== stopByte) {
            stopPosition++;
        }
        if (stopPosition >= len) {
            throw new errors_ts_1.CramBufferOverrunError('byteArrayStop reading beyond length of data buffer?');
        }
        cursor.bytePosition = stopPosition + 1;
        return dataBuffer.subarray(startPosition, stopPosition);
    }
}
exports.default = ByteArrayStopCodec;
//# sourceMappingURL=byteArrayStop.js.map