@gmod/cram 6.0.0 → 7.0.0

package/esm/htscodecs/rans.js

@@ -1,218 +0,0 @@
-/* eslint-disable no-var */
-// @ts-nocheck
-/*
- * 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.
- */
-import IOStream from "./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.
-export function decode(src) {
-    const stream = new IOStream(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/esm/htscodecs/rans.js.map

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

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

package/esm/htscodecs/rans4x16.js

@@ -1,439 +0,0 @@
-/* eslint-disable no-var */
-// @ts-nocheck
-/*
- * 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.
- */
-import IOStream from "./iostream.js";
-// ----------------------------------------------------------------------
-// rANS primitives itself
-//
-// RansGet* is decoder side
-function RansGetCumulativeFreq(R, bits) {
-    return R & ((1 << bits) - 1);
-}
-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++;
-    }
-    // console.error(f, C, s)
-    return s;
-}
-function RansBuildC2S(C, bits) {
-    const max = 1 << bits;
-    const C2S = new Array(max);
-    let s = 0;
-    for (let f = 0; f < max; f++) {
-        while (f >= C[s + 1]) {
-            s++;
-        }
-        C2S[f] = s;
-    }
-    return C2S;
-}
-function RansAdvanceStep(R, c, f, bits) {
-    return f * (R >> bits) + (R & ((1 << bits) - 1)) - c;
-}
-function RansRenorm(src, R) {
-    if (R < 1 << 15) {
-        R = (R << 16) + src.ReadUint16();
-    }
-    return R;
-}
-function DecodeRLEMeta(src, N) {
-    const u_meta_len = src.ReadUint7();
-    const rle_len = src.ReadUint7();
-    // Decode RLE lengths
-    if (u_meta_len & 1) {
-        var rle_meta = src.ReadData((u_meta_len - 1) / 2);
-    }
-    else {
-        const comp_meta_len = src.ReadUint7();
-        var rle_meta = src.ReadData(comp_meta_len);
-        rle_meta = RansDecode0(new IOStream(rle_meta), u_meta_len / 2, N);
-    }
-    // Decode list of symbols for which RLE lengths are applied
-    var rle_meta = new IOStream(rle_meta);
-    const L = new Array(256);
-    let n = rle_meta.ReadByte();
-    if (n == 0) {
-        n = 256;
-    }
-    for (let i = 0; i < n; i++) {
-        L[rle_meta.ReadByte()] = 1;
-    }
-    return [L, rle_meta, rle_len];
-}
-function DecodeRLE(buf, L, rle_meta, len) {
-    const src = new IOStream(buf);
-    const out = new Uint8Array(len);
-    // Expand up buf+meta to out; i = buf index, j = out index
-    let j = 0;
-    for (let i = 0; j < len; i++) {
-        const sym = buf[i];
-        if (L[sym]) {
-            const run = rle_meta.ReadUint7();
-            for (let r = 0; r <= run; r++) {
-                out[j++] = sym;
-            }
-        }
-        else {
-            out[j++] = sym;
-        }
-    }
-    return out;
-}
-// Pack meta data is the number and value of distinct symbols plus
-// the length of the packed byte stream.
-function DecodePackMeta(src) {
-    const nsym = src.ReadByte();
-    const P = new Array(nsym);
-    for (let i = 0; i < nsym; i++) {
-        P[i] = src.ReadByte();
-    }
-    const len = src.ReadUint7();
-    return [P, nsym, len];
-}
-// Extract bits from src producing output of length len.
-// Nsym is number of distinct symbols used.
-function DecodePack(data, P, nsym, len) {
-    const out = new Uint8Array(len);
-    let j = 0;
-    // Constant value
-    if (nsym <= 1) {
-        for (var i = 0; i < len; i++) {
-            out[i] = P[0];
-        }
-    }
-    // 1 bit per value
-    else if (nsym <= 2) {
-        for (i = 0; i < len; i++) {
-            if (i % 8 == 0) {
-                var v = data[j++];
-            }
-            out[i] = P[v & 1];
-            v >>= 1;
-        }
-    }
-    // 2 bits per value
-    else if (nsym <= 4) {
-        for (i = 0; i < len; i++) {
-            if (i % 4 == 0) {
-                var v = data[j++];
-            }
-            out[i] = P[v & 3];
-            v >>= 2;
-        }
-    }
-    // 4 bits per value
-    else if (nsym <= 16) {
-        for (i = 0; i < len; i++) {
-            if (i % 2 == 0) {
-                var v = data[j++];
-            }
-            out[i] = P[v & 15];
-            v >>= 4;
-        }
-    }
-    return out;
-}
-function RansDecodeStripe(src, len) {
-    const N = src.ReadByte();
-    // Retrieve lengths
-    const clen = new Array(N);
-    const ulen = new Array(N);
-    for (var j = 0; j < N; j++) {
-        clen[j] = src.ReadUint7();
-    }
-    // Decode streams
-    const T = new Array(N);
-    for (var j = 0; j < N; j++) {
-        ulen[j] = Math.floor(len / N) + (len % N > j);
-        T[j] = RansDecodeStream(src, ulen[j]);
-    }
-    // Transpose
-    const out = new Uint8Array(len);
-    for (var j = 0; j < N; j++) {
-        for (let i = 0; i < ulen[j]; i++) {
-            out[i * N + j] = T[j][i];
-        }
-    }
-    return out;
-}
-// ----------------------------------------------------------------------
-// Main rANS entry function: decodes a compressed src and
-// returns the uncompressed buffer.
-export function decode(src) {
-    const stream = new IOStream(src);
-    return RansDecodeStream(stream, 0);
-}
-function RansDecodeStream(stream, n_out) {
-    const format = stream.ReadByte();
-    const order = format & 1;
-    const x32 = format & 4;
-    const stripe = format & 8;
-    const nosz = format & 16;
-    const cat = format & 32;
-    const rle = format & 64;
-    const pack = format & 128;
-    const Nway = x32 ? 32 : 4;
-    if (!nosz) {
-        n_out = stream.ReadUint7();
-    }
-    // N-way interleaving
-    if (stripe) {
-        return RansDecodeStripe(stream, n_out);
-    }
-    // Bit packing
-    if (pack) {
-        var pack_len = n_out;
-        var [P, nsym, n_out] = DecodePackMeta(stream);
-    }
-    // Run length encoding
-    if (rle) {
-        var rle_len = n_out;
-        var [L, rle_meta, n_out] = DecodeRLEMeta(stream, Nway);
-    }
-    // Uncompress data (all, packed or run literals)
-    if (cat) {
-        var buf = stream.ReadData(n_out);
-    }
-    else if (order == 0) {
-        var buf = RansDecode0(stream, n_out, Nway);
-    }
-    else {
-        var buf = RansDecode1(stream, n_out, Nway);
-    }
-    // Apply expansion transforms
-    if (rle) {
-        buf = DecodeRLE(buf, L, rle_meta, rle_len);
-    }
-    if (pack) {
-        buf = DecodePack(buf, P, nsym, pack_len);
-    }
-    return buf;
-}
-// ----------------------------------------------------------------------
-// Order-0 decoder
-function ReadAlphabet(src) {
-    const A = new Array(256);
-    for (let i = 0; i < 256; i++) {
-        A[i] = 0;
-    }
-    let rle = 0;
-    let sym = src.ReadByte();
-    let last_sym = sym;
-    do {
-        A[sym] = 1;
-        if (rle > 0) {
-            rle--;
-            sym++;
-        }
-        else {
-            sym = src.ReadByte();
-            if (sym == last_sym + 1) {
-                rle = src.ReadByte();
-            }
-        }
-        last_sym = sym;
-    } while (sym != 0);
-    return A;
-}
-// 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;
-    }
-    // Fetch alphabet
-    const A = ReadAlphabet(src);
-    // Fetch frequencies for the symbols listed in our alphabet
-    for (var i = 0; i < 256; i++) {
-        if (A[i] > 0) {
-            F[i] = src.ReadUint7();
-        }
-    }
-    NormaliseFrequencies0_Shift(F, 12);
-    // 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, N) {
-    // 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, 12);
-    // Initialise rANS state
-    const R = new Array(N);
-    for (var i = 0; i < N; i++) {
-        R[i] = src.ReadUint32();
-    }
-    // Main decode loop
-    const output = new Uint8Array(nbytes);
-    for (var i = 0; i < nbytes; i++) {
-        const ix = i & (N - 1); // equiv to i%N as N is power of 2
-        const f = RansGetCumulativeFreq(R[ix], 12);
-        const s = C2S[f]; // Equiv to RansGetSymbolFromFreq(C, f);
-        output[i] = s;
-        R[ix] = RansAdvanceStep(R[ix], C[s], F[s], 12);
-        R[ix] = RansRenorm(src, R[ix]);
-    }
-    // Main decode loop
-    return output;
-}
-function NormaliseFrequencies0_Shift(F, bits) {
-    // Compute total and number of bits to shift by
-    let tot = 0;
-    for (var i = 0; i < 256; i++) {
-        tot += F[i];
-    }
-    if (tot == 0 || tot == 1 << bits) {
-        return;
-    }
-    let shift = 0;
-    while (tot < 1 << bits) {
-        tot *= 2;
-        shift++;
-    }
-    // Scale total of frequencies to (1<<bits)
-    for (var i = 0; i < 256; i++) {
-        F[i] <<= shift;
-    }
-}
-// ----------------------------------------------------------------------
-// Order-1 decoder
-// Decode a table of order-1 frequencies,
-// filling out the F and C arrays.
-function ReadFrequencies1(src, F, C, shift) {
-    // Initialise; not in the specification - implicit?
-    for (var i = 0; i < 256; i++) {
-        F[i] = new Array(256);
-        C[i] = new Array(256);
-        for (var j = 0; j < 256; j++) {
-            F[i][j] = 0;
-        }
-    }
-    // Fetch alphabet
-    const A = ReadAlphabet(src);
-    // Read F[]
-    for (var i = 0; i < 256; i++) {
-        if (!A[i]) {
-            continue;
-        }
-        let run = 0;
-        for (var j = 0; j < 256; j++) {
-            if (!A[j]) {
-                continue;
-            }
-            if (run > 0) {
-                run--;
-            }
-            else {
-                F[i][j] = src.ReadUint7();
-                if (F[i][j] == 0) {
-                    run = src.ReadByte();
-                }
-            }
-        }
-        NormaliseFrequencies0_Shift(F[i], shift);
-        // Compute C[] from F[]
-        C[i][0] = 0;
-        for (var j = 0; j < 256; j++) {
-            C[i][j + 1] = C[i][j] + F[i][j];
-        }
-    }
-}
-function RansDecode1(src, nbytes, N) {
-    // FIXME: this bit is missing from the RansDecode0 pseudocode.
-    var comp = src.ReadByte();
-    const shift = comp >> 4;
-    var freq_src = src;
-    if (comp & 1) {
-        const ulen = src.ReadUint7();
-        const clen = src.ReadUint7();
-        var comp = new IOStream(src.ReadData(clen));
-        var freq_src = new IOStream(RansDecode0(comp, ulen, 4));
-    }
-    // Decode frequencies
-    const F = new Array(256);
-    const C = new Array(256);
-    ReadFrequencies1(freq_src, F, C, shift);
-    // Fast lookup to avoid slow RansGetSymbolFromFreq
-    const C2S = new Array(256);
-    for (var i = 0; i < 256; i++ // Could do only for symbols in alphabet?
-    ) {
-        C2S[i] = RansBuildC2S(C[i], shift);
-    }
-    // Initialise rANS state
-    const R = new Array(N);
-    const L = new Array(N);
-    for (var j = 0; j < N; j++) {
-        R[j] = src.ReadUint32();
-        L[j] = 0;
-    }
-    // Main decode loop
-    const output = new Uint8Array(nbytes);
-    const nbytesx = Math.floor(nbytes / N);
-    for (var i = 0; i < nbytesx; i++) {
-        for (var j = 0; j < N; j++) {
-            var f = RansGetCumulativeFreq(R[j], shift);
-            // var s = RansGetSymbolFromFreq(C[L[j]], f);
-            var s = C2S[L[j]][f]; // Precomputed version of above
-            output[i + j * nbytesx] = s;
-            R[j] = RansAdvanceStep(R[j], C[L[j]][s], F[L[j]][s], shift);
-            R[j] = RansRenorm(src, R[j]);
-            L[j] = s;
-        }
-    }
-    // Now deal with the remainder if buffer size is not a multiple of N,
-    // using the last rANS state exclusively.  (It'd have been nice to have
-    // designed this to just act as if we kept going with a bail out.)
-    i = N * i;
-    while (i < nbytes) {
-        var f = RansGetCumulativeFreq(R[N - 1], shift);
-        var s = RansGetSymbolFromFreq(C[L[N - 1]], f);
-        output[i++] = s;
-        R[N - 1] = RansAdvanceStep(R[N - 1], C[L[N - 1]][s], F[L[N - 1]][s], shift);
-        R[N - 1] = RansRenorm(src, R[N - 1]);
-        L[N - 1] = s;
-    }
-    return output;
-}
-//# sourceMappingURL=rans4x16.js.map