@gmod/cram 3.0.6 → 4.0.0

package/dist/htscodecs/rans4x16.js

@@ -0,0 +1,405 @@
+"use strict";
+/*
+ * 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 = require('./iostream');
+//----------------------------------------------------------------------
+// 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.
+    var s = 0;
+    while (f >= C[s + 1])
+        s++;
+    //console.error(f, C, s)
+    return s;
+}
+function RansBuildC2S(C, bits) {
+    var max = 1 << bits;
+    var C2S = new Array(max);
+    var s = 0;
+    for (var 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) {
+    var u_meta_len = src.ReadUint7();
+    var rle_len = src.ReadUint7();
+    // Decode RLE lengths
+    if (u_meta_len & 1) {
+        var rle_meta = src.ReadData((u_meta_len - 1) / 2);
+    }
+    else {
+        var 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);
+    var L = new Array(256);
+    var n = rle_meta.ReadByte();
+    if (n == 0)
+        n = 256;
+    for (var i = 0; i < n; i++)
+        L[rle_meta.ReadByte()] = 1;
+    return [L, rle_meta, rle_len];
+}
+function DecodeRLE(buf, L, rle_meta, len) {
+    var src = new IOStream(buf);
+    var out = new Uint8Array(len);
+    // Expand up buf+meta to out; i = buf index, j = out index
+    var j = 0;
+    for (var i = 0; j < len; i++) {
+        var sym = buf[i];
+        if (L[sym]) {
+            var run = rle_meta.ReadUint7();
+            for (var 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) {
+    var nsym = src.ReadByte();
+    var P = new Array(nsym);
+    for (var i = 0; i < nsym; i++)
+        P[i] = src.ReadByte();
+    var 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) {
+    var out = new Uint8Array(len);
+    var 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) {
+    var N = src.ReadByte();
+    // Retrieve lengths
+    var clen = new Array(N);
+    var ulen = new Array(N);
+    for (var j = 0; j < N; j++)
+        clen[j] = src.ReadUint7();
+    // Decode streams
+    var 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
+    var out = new Uint8Array(len);
+    for (var j = 0; j < N; j++) {
+        for (var 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.
+function decode(src) {
+    var stream = new IOStream(src);
+    return RansDecodeStream(stream, 0);
+}
+function RansDecodeStream(stream, n_out) {
+    var format = stream.ReadByte();
+    var order = format & 1;
+    var x32 = format & 4;
+    var stripe = format & 8;
+    var nosz = format & 16;
+    var cat = format & 32;
+    var rle = format & 64;
+    var pack = format & 128;
+    var 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) {
+    var A = new Array(256);
+    for (var i = 0; i < 256; i++)
+        A[i] = 0;
+    var rle = 0;
+    var sym = src.ReadByte();
+    var 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 frequences,
+// 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
+    var 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
+    var F = new Array(256);
+    var C = new Array(256);
+    ReadFrequencies0(src, F, C);
+    // Fast lookup to avoid slow RansGetSymbolFromFreq
+    var C2S = RansBuildC2S(C, 12);
+    // Initialise rANS state
+    var R = new Array(N);
+    for (var i = 0; i < N; i++)
+        R[i] = src.ReadUint32();
+    // Main decode loop
+    var output = new Uint8Array(nbytes);
+    for (var i = 0; i < nbytes; i++) {
+        var ix = i & (N - 1); // equiv to i%N as N is power of 2
+        var f = RansGetCumulativeFreq(R[ix], 12);
+        var 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
+    var tot = 0;
+    for (var i = 0; i < 256; i++)
+        tot += F[i];
+    if (tot == 0 || tot == 1 << bits)
+        return;
+    var 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 frequences,
+// 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
+    var A = ReadAlphabet(src);
+    // Read F[]
+    for (var i = 0; i < 256; i++) {
+        if (!A[i])
+            continue;
+        var 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();
+    var shift = comp >> 4;
+    var freq_src = src;
+    if (comp & 1) {
+        var ulen = src.ReadUint7();
+        var clen = src.ReadUint7();
+        var comp = new IOStream(src.ReadData(clen));
+        var freq_src = new IOStream(RansDecode0(comp, ulen, 4));
+    }
+    // Decode frequencies
+    var F = new Array(256);
+    var C = new Array(256);
+    ReadFrequencies1(freq_src, F, C, shift);
+    // Fast lookup to avoid slow RansGetSymbolFromFreq
+    var 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
+    var R = new Array(N);
+    var L = new Array(N);
+    for (var j = 0; j < N; j++) {
+        R[j] = src.ReadUint32();
+        L[j] = 0;
+    }
+    // Main decode loop
+    var output = new Uint8Array(nbytes);
+    var 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;
+}
+module.exports = { decode };
+//# sourceMappingURL=rans4x16.js.map

package/dist/htscodecs/rans4x16.js.map

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package/dist/htscodecs/tok3.d.ts

@@ -0,0 +1,2 @@
+export function encode(src: any, use_arith: any): any;
+export function decode(src: any, len: any, separator: any): string;