@gmod/cram/dist/htscodecs/index.js

read CRAM files with pure Javascript

"use strict";
// @ts-nocheck
//
/*
 * Copyright (c) 2020 Genome Research Ltd.
 * Author(s): James Bonfield
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 *    1. Redistributions of source code must retain the above copyright notice,
 *       this list of conditions and the following disclaimer.
 *
 *    2. Redistributions in binary form must reproduce the above
 *       copyright notice, this list of conditions and the following
 *       disclaimer in the documentation and/or other materials provided
 *       with the distribution.
 *
 *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
 *       Institute nor the names of its contributors may be used to endorse
 *       or promote products derived from this software without specific
 *       prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
 * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
 * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
 * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
 * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
    if (k2 === undefined) k2 = k;
    var desc = Object.getOwnPropertyDescriptor(m, k);
    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
      desc = { enumerable: true, get: function() { return m[k]; } };
    }
    Object.defineProperty(o, k2, desc);
}) : (function(o, m, k, k2) {
    if (k2 === undefined) k2 = k;
    o[k2] = m[k];
}));
var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
    Object.defineProperty(o, "default", { enumerable: true, value: v });
}) : function(o, v) {
    o["default"] = v;
});
var __importStar = (this && this.__importStar) || (function () {
    var ownKeys = function(o) {
        ownKeys = Object.getOwnPropertyNames || function (o) {
            var ar = [];
            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
            return ar;
        };
        return ownKeys(o);
    };
    return function (mod) {
        if (mod && mod.__esModule) return mod;
        var result = {};
        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
        __setModuleDefault(result, mod);
        return result;
    };
})();
var __importDefault = (this && this.__importDefault) || function (mod) {
    return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
exports.r4x8_uncompress = r4x8_uncompress;
exports.r4x16_uncompress = r4x16_uncompress;
exports.arith_uncompress = arith_uncompress;
exports.fqzcomp_uncompress = fqzcomp_uncompress;
exports.tok3_uncompress = tok3_uncompress;
// This is an interface to the htscodecs reference implementation of
// the CRAM 3.1 codecs.
// This JavaScript file is not part of the reference implementation
// and is simply and interface to get a consistent interface for cram-js.
const arith_gen_ts_1 = __importDefault(require("./arith_gen.js"));
const fqzcomp = __importStar(require("./fqzcomp.js"));
const r4x8 = __importStar(require("./rans.js"));
const r4x16 = __importStar(require("./rans4x16.js"));
const tok3 = __importStar(require("./tok3.js"));
function r4x8_uncompress(inputBuffer) {
    return r4x8.decode(inputBuffer);
}
function r4x16_uncompress(inputBuffer) {
    return r4x16.decode(inputBuffer);
}
function arith_uncompress(inputBuffer) {
    // fix by @cmdcolin for CRAM 3.1
    // xref https://github.com/jkbonfield/htscodecs/pull/1/files
    return new arith_gen_ts_1.default().decode(inputBuffer);
}
function fqzcomp_uncompress(inputBuffer) {
    const q_lens = [];
    return fqzcomp.decode(inputBuffer, q_lens);
}
function tok3_uncompress(inputBuffer) {
    // Returns in string form instead of buffer
    const out = tok3.decode(inputBuffer, 0, '\0');
    return Uint8Array.from(Array.from(out).map(letter => letter.charCodeAt(0)));
}
//# sourceMappingURL=index.js.map