@gmod/cram/dist/cramFile/codecs/external.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");
const util_ts_1 = require("../util.js");
const getBits_ts_1 = require("./getBits.js");
class ExternalCodec extends _base_ts_1.default {
    constructor(parameters, dataType) {
        super(parameters, dataType);
        if (this.dataType === 'int') {
            this._decodeData = this._decodeInt;
        }
        else if (this.dataType === 'byte') {
            this._decodeData = this._decodeByte;
        }
        else {
            throw new errors_ts_1.CramUnimplementedError(`${this.dataType} decoding not yet implemented by EXTERNAL codec`);
        }
    }
    decode(_slice, _coreDataBlock, blocksByContentId, cursors) {
        const { blockContentId } = this.parameters;
        const contentBlock = blocksByContentId[blockContentId];
        return contentBlock
            ? this._decodeData(contentBlock, cursors.externalBlocks.getCursor(blockContentId))
            : undefined;
    }
    _decodeInt(contentBlock, cursor) {
        const [result, bytesRead] = (0, util_ts_1.parseItf8)(contentBlock.content, cursor.bytePosition);
        cursor.bytePosition = cursor.bytePosition + bytesRead;
        return result;
    }
    _decodeByte(contentBlock, cursor) {
        if (cursor.bytePosition >= contentBlock.content.length) {
            throw new getBits_ts_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
        }
        return contentBlock.content[cursor.bytePosition++];
    }
}
exports.default = ExternalCodec;
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