@gmod/cram 6.0.0 → 7.0.0

package/dist/htscodecs/iostream.js

@@ -1,148 +0,0 @@
-"use strict";
-// @ts-nocheck
-Object.defineProperty(exports, "__esModule", { value: true });
-/*
- * Copyright (c) 2019 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.
- */
-// Turn a buffer into a fake stream with get / put commands.
-// This enables up to closely match the published pseudocode.
-class IOStream {
-    constructor(buf, start_pos = 0, size = 0) {
-        if (size !== 0) {
-            this.buf = new Uint8Array(size);
-            this.length = size;
-        }
-        else {
-            this.buf = buf;
-            this.length = buf.length;
-        }
-        this.dataView = new DataView(this.buf.buffer);
-        this.pos = start_pos;
-    }
-    // ----------
-    // Reading
-    EOF() {
-        return this.pos >= this.length;
-    }
-    ReadData(len) {
-        const A = this.buf.slice(this.pos, this.pos + len);
-        this.pos += len;
-        return A;
-    }
-    ReadByte() {
-        const b = this.buf[this.pos];
-        this.pos++;
-        return b;
-    }
-    ReadChar() {
-        const b = this.buf[this.pos];
-        this.pos++;
-        return String.fromCharCode(b);
-    }
-    ReadUint16() {
-        let i = this.ReadByte();
-        i |= this.ReadByte() << 8;
-        return i;
-    }
-    ReadUint32() {
-        const i = this.dataView.getInt32(this.pos, true);
-        this.pos += 4;
-        return i;
-    }
-    // nul terminated string
-    ReadString() {
-        let s = '';
-        let b;
-        do {
-            b = this.buf[this.pos++];
-            if (b) {
-                s += String.fromCharCode(b);
-            }
-        } while (b);
-        return s;
-    }
-    ReadUint7() {
-        // Variable sized unsigned integers
-        let i = 0;
-        let c;
-        do {
-            c = this.ReadByte();
-            i = (i << 7) | (c & 0x7f);
-        } while (c & 0x80);
-        return i;
-    }
-    ReadITF8() {
-        let i = this.buf[this.pos];
-        this.pos++;
-        // process.stderr.write("i="+i+"\n");
-        if (i >= 0xf0) {
-            // 1111xxxx => +4 bytes
-            i = (i & 0x0f) << 28;
-            i +=
-                (this.buf[this.pos + 0] << 20) +
-                    (this.buf[this.pos + 1] << 12) +
-                    (this.buf[this.pos + 2] << 4) +
-                    (this.buf[this.pos + 3] >> 4);
-            this.pos += 4;
-            // process.stderr.write("  4i="+i+"\n");
-        }
-        else if (i >= 0xe0) {
-            // 1110xxxx => +3 bytes
-            i = (i & 0x0f) << 24;
-            i +=
-                (this.buf[this.pos + 0] << 16) +
-                    (this.buf[this.pos + 1] << 8) +
-                    (this.buf[this.pos + 2] << 0);
-            this.pos += 3;
-            // process.stderr.write("  3i="+i+"\n");
-        }
-        else if (i >= 0xc0) {
-            // 110xxxxx => +2 bytes
-            i = (i & 0x1f) << 16;
-            i += (this.buf[this.pos + 0] << 8) + (this.buf[this.pos + 1] << 0);
-            this.pos += 2;
-            // process.stderr.write("  2i="+i+"\n");
-        }
-        else if (i >= 0x80) {
-            // 10xxxxxx => +1 bytes
-            i = (i & 0x3f) << 8;
-            i += this.buf[this.pos];
-            this.pos++;
-        }
-        else {
-            // 0xxxxxxx => +0 bytes
-        }
-        return i;
-    }
-}
-exports.default = IOStream;
-//# sourceMappingURL=iostream.js.map

package/dist/htscodecs/iostream.js.map

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package/dist/htscodecs/rans.d.ts

@@ -1 +0,0 @@
-export declare function decode(src: any): Uint8Array<any>;

package/dist/htscodecs/rans.js

@@ -1,224 +0,0 @@
-"use strict";
-/* eslint-disable no-var */
-// @ts-nocheck
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.decode = decode;
-/*
- * Copyright (c) 2019-2020 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.
- */
-const iostream_ts_1 = __importDefault(require("./iostream.js"));
-// ----------------------------------------------------------------------
-// rANS primitives itself
-//
-// RansGet* is decoder side
-function RansGetCumulativeFreq(R) {
-    return R & 0xfff;
-}
-function RansGetSymbolFromFreq(C, f) {
-    // NOTE: Inefficient.
-    // In practice we would implement this via a precomputed
-    // lookup table C2S[f]; see RansBuildC2S below.
-    let s = 0;
-    while (f >= C[s + 1]) {
-        s++;
-    }
-    return s;
-}
-function RansBuildC2S(C) {
-    const C2S = new Array(0x1000);
-    let s = 0;
-    for (let f = 0; f < 0x1000; f++) {
-        while (f >= C[s + 1]) {
-            s++;
-        }
-        C2S[f] = s;
-    }
-    return C2S;
-}
-function RansAdvanceStep(R, c, f) {
-    return f * (R >> 12) + (R & 0xfff) - c;
-}
-function RansRenorm(src, R) {
-    while (R < 1 << 23) {
-        R = (R << 8) + src.ReadByte();
-    }
-    return R;
-}
-// ----------------------------------------------------------------------
-// Main rANS entry function: decodes a compressed src and
-// returns the uncompressed buffer.
-function decode(src) {
-    const stream = new iostream_ts_1.default(src);
-    const order = stream.ReadByte();
-    const n_in = stream.ReadUint32();
-    const n_out = stream.ReadUint32();
-    return order == 0 ? RansDecode0(stream, n_out) : RansDecode1(stream, n_out);
-}
-// ----------------------------------------------------------------------
-// Order-0 decoder
-// Decode a single table of order-0 frequencies,
-// filling out the F and C arrays.
-function ReadFrequencies0(src, F, C) {
-    // Initialise; not in the specification - implicit?
-    for (var i = 0; i < 256; i++) {
-        F[i] = 0;
-    }
-    let sym = src.ReadByte();
-    let last_sym = sym;
-    let rle = 0;
-    // Read F[]
-    do {
-        const f = src.ReadITF8();
-        F[sym] = f;
-        if (rle > 0) {
-            rle--;
-            sym++;
-        }
-        else {
-            sym = src.ReadByte();
-            if (sym == last_sym + 1) {
-                rle = src.ReadByte();
-            }
-        }
-        last_sym = sym;
-    } while (sym != 0);
-    // Compute C[] from F[]
-    C[0] = 0;
-    for (var i = 0; i <= 255; i++) {
-        C[i + 1] = C[i] + F[i];
-    }
-}
-function RansDecode0(src, nbytes) {
-    // Decode frequencies
-    const F = new Array(256);
-    const C = new Array(256);
-    ReadFrequencies0(src, F, C);
-    // Fast lookup to avoid slow RansGetSymbolFromFreq
-    const C2S = RansBuildC2S(C);
-    // Initialise rANS state
-    const R = new Array(4);
-    for (var i = 0; i < 4; i++) {
-        R[i] = src.ReadUint32();
-    }
-    // Main decode loop
-    const output = new Uint8Array(nbytes);
-    for (var i = 0; i < nbytes; i++) {
-        const i4 = i % 4;
-        const f = RansGetCumulativeFreq(R[i4]);
-        const s = C2S[f]; // Equiv to RansGetSymbolFromFreq(C, f);
-        output[i] = s;
-        R[i4] = RansAdvanceStep(R[i4], C[s], F[s]);
-        R[i4] = RansRenorm(src, R[i4]);
-    }
-    return output;
-}
-// ----------------------------------------------------------------------
-// Order-1 decoder
-// Decode a table of order-1 frequencies,
-// filling out the F and C arrays.
-function ReadFrequencies1(src, F, C) {
-    // Initialise; not in the specification - implicit?
-    for (let i = 0; i < 256; i++) {
-        F[i] = new Array(256);
-        C[i] = new Array(256);
-        for (let j = 0; j < 256; j++) {
-            F[i][j] = 0;
-        }
-    }
-    let sym = src.ReadByte();
-    let last_sym = sym;
-    let rle = 0;
-    // Read F[]
-    do {
-        ReadFrequencies0(src, F[sym], C[sym]);
-        if (rle > 0) {
-            rle--;
-            sym++;
-        }
-        else {
-            sym = src.ReadByte();
-            if (sym == last_sym + 1) {
-                rle = src.ReadByte();
-            }
-        }
-        last_sym = sym;
-    } while (sym != 0);
-}
-function RansDecode1(src, nbytes) {
-    // Decode frequencies
-    const F = new Array(256);
-    const C = new Array(256);
-    ReadFrequencies1(src, F, C);
-    // Fast lookup to avoid slow RansGetSymbolFromFreq
-    const C2S = new Array(256);
-    for (var i = 0; i < 256; i++) {
-        C2S[i] = RansBuildC2S(C[i]);
-    }
-    // Initialise rANS state
-    const R = new Array(4);
-    const L = new Array(4);
-    for (var j = 0; j < 4; j++) {
-        R[j] = src.ReadUint32();
-        L[j] = 0;
-    }
-    // Main decode loop
-    const output = new Uint8Array(nbytes);
-    const nbytes4 = Math.floor(nbytes / 4);
-    for (var i = 0; i < nbytes4; i++) {
-        for (var j = 0; j < 4; j++) {
-            var f = RansGetCumulativeFreq(R[j]);
-            // var s = RansGetSymbolFromFreq(C[L[j]], f);
-            var s = C2S[L[j]][f]; // Precomputed version of above
-            output[i + j * nbytes4] = s;
-            R[j] = RansAdvanceStep(R[j], C[L[j]][s], F[L[j]][s]);
-            R[j] = RansRenorm(src, R[j]);
-            L[j] = s;
-        }
-    }
-    // Now deal with the remainder if buffer size is not a multiple of 4,
-    // using rANS state 3 exclusively.  (It'd have been nice to have
-    // designed this to just act as if we kept going with a bail out.)
-    i = 4 * i;
-    while (i < nbytes) {
-        var f = RansGetCumulativeFreq(R[3]);
-        var s = RansGetSymbolFromFreq(C[L[3]], f);
-        output[i++] = s;
-        R[3] = RansAdvanceStep(R[3], C[L[3]][s], F[L[3]][s]);
-        R[3] = RansRenorm(src, R[3]);
-        L[3] = s;
-    }
-    return output;
-}
-//# sourceMappingURL=rans.js.map

package/dist/htscodecs/rans.js.map

@@ -1 +0,0 @@
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package/dist/htscodecs/rans4x16.d.ts

@@ -1 +0,0 @@
-export declare function decode(src: any): any;