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

read CRAM files with pure Javascript

import CramCodec from "./_base.js";
import { CramUnimplementedError } from "../../errors.js";
import { parseItf8 } from "../util.js";
import { CramBufferOverrunError } from "./getBits.js";
export default class ExternalCodec extends CramCodec {
    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 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] = parseItf8(contentBlock.content, cursor.bytePosition);
        cursor.bytePosition = cursor.bytePosition + bytesRead;
        return result;
    }
    _decodeByte(contentBlock, cursor) {
        if (cursor.bytePosition >= contentBlock.content.length) {
            throw new CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
        }
        return contentBlock.content[cursor.bytePosition++];
    }
}
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