@gmod/cram
Version:
read CRAM files with pure Javascript
37 lines • 1.71 kB
JavaScript
;
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 getBits_ts_1 = require("./getBits.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;
// 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 getBits_ts_1.CramBufferOverrunError('byteArrayStop reading beyond length of data buffer?');
}
stopPosition = stopPosition + 1;
}
cursor.bytePosition = stopPosition + 1;
return dataBuffer.subarray(startPosition, stopPosition);
}
}
exports.default = ByteArrayStopCodec;
//# sourceMappingURL=byteArrayStop.js.map