@gmod/cram 3.0.6 → 3.0.7

package/dist/htscodecs/rans.js

@@ -0,0 +1,480 @@
+"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) {
+    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.
+    var s = 0;
+    while (f >= C[s + 1])
+        s++;
+    return s;
+}
+function RansBuildC2S(C) {
+    var C2S = new Array(0x1000);
+    var s = 0;
+    for (var 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;
+}
+// RanEnc* is for encoder
+function RansEncInit() {
+    return 1 << 23;
+}
+function RansEncFlush(R, dst) {
+    dst.WriteByteNeg((R >> 24) & 0xff);
+    dst.WriteByteNeg((R >> 16) & 0xff);
+    dst.WriteByteNeg((R >> 8) & 0xff);
+    dst.WriteByteNeg((R >> 0) & 0xff);
+}
+function RansEncRenorm(R, dst, freq, scale_bits) {
+    var R_max = (((1 << 23) >> scale_bits) << 8) * freq;
+    while (R >= R_max) {
+        dst.WriteByteNeg(R & 0xff);
+        R >>= 8;
+    }
+    return R;
+}
+// Puts a symbol with frequency freq, cumulative freq start
+// and total freq 1<<scale_bits.
+//
+// Note with static probabilities, /freq and %freq could be
+// precomputed via multiplies and shifts.
+function RansEncPut(R, dst, start, freq, scale_bits) {
+    var scale = 1 << scale_bits;
+    R = RansEncRenorm(R, dst, freq, scale_bits);
+    R = (Math.floor(R / freq) << scale_bits) + (R % freq) + start;
+    return R;
+}
+//----------------------------------------------------------------------
+// Main rANS entry function: decodes a compressed src and
+// returns the uncompressed buffer.
+function decode(src) {
+    var stream = new IOStream(src);
+    var order = stream.ReadByte();
+    var n_in = stream.ReadUint32();
+    var n_out = stream.ReadUint32();
+    if (order == 0) {
+        return RansDecode0(stream, n_out);
+    }
+    else {
+        return RansDecode1(stream, n_out);
+    }
+}
+function encode(src, order) {
+    //var stream = new IOStream(src);
+    //var n_in  = stream.ReadUint32();
+    //var n_out = stream.ReadUint32();
+    if (order == 0) {
+        return RansEncode0(src);
+    }
+    else {
+        return RansEncode1(src);
+    }
+}
+//----------------------------------------------------------------------
+// Order-0 decoder
+// 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;
+    var sym = src.ReadByte();
+    var last_sym = sym;
+    var rle = 0;
+    // Read F[]
+    do {
+        var 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
+    var F = new Array(256);
+    var C = new Array(256);
+    ReadFrequencies0(src, F, C);
+    // Fast lookup to avoid slow RansGetSymbolFromFreq
+    var C2S = RansBuildC2S(C);
+    // Initialise rANS state
+    var R = new Array(4);
+    for (var i = 0; i < 4; i++)
+        R[i] = src.ReadUint32();
+    // Main decode loop
+    var output = new Buffer.allocUnsafe(nbytes);
+    for (var i = 0; i < nbytes; i++) {
+        var i4 = i % 4;
+        var f = RansGetCumulativeFreq(R[i4]);
+        var 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-0 encoder
+function BuildFrequencies0(src, F) {
+    for (var i = 0; i < 256; i++)
+        F[i] = 0;
+    for (var i = 0; i < src.length; i++)
+        F[src[i]]++;
+}
+function NormaliseFrequencies0(F) {
+    // Compute total
+    var tot = 0;
+    for (var i = 0; i < 256; i++)
+        tot += F[i];
+    // Scale total of frequencies to max
+    const max = 1 << 12;
+    var scale = max / tot;
+    do {
+        var max_val = 0;
+        var max_idx = 0;
+        var renorm = 0;
+        tot = 0;
+        for (var i = 0; i < 256; i++) {
+            if (F[i] == 0)
+                continue;
+            if (max_val < F[i]) {
+                max_val = F[i];
+                max_idx = i;
+            }
+            F[i] = Math.floor(F[i] * scale);
+            if (F[i] == 0)
+                F[i] = 1;
+            tot += F[i];
+        }
+        // Adjust new tot to ensure it matches.
+        if (tot < max) {
+            // Too low, boost the most common symbol
+            F[max_idx] += max - tot;
+        }
+        else if (tot - max < F[max_idx] / 2 && F[max_idx] > 2) {
+            // Too high, reduce the common symbol
+            F[max_idx] -= tot - max;
+        }
+        else if (tot != max) {
+            // Much too high, fudge scale and try again.
+            scale = scale * 0.99;
+            renorm = 1;
+        }
+    } while (renorm);
+}
+function WriteFrequencies0(out, F) {
+    var rle = 0;
+    for (var i = 0; i < 256; i++) {
+        if (!F[i])
+            continue;
+        // Output Symbol if needed and Frequency
+        if (rle > 0)
+            rle--;
+        else {
+            out.WriteByte(i);
+            if (i > 0 && F[i - 1] > 0) {
+                // We've encoded two symbol frequencies in a row.
+                // How many more are there?  Store that count so
+                // we can avoid writing consecutive symbols.
+                for (rle = i + 1; rle < 256 && F[rle]; rle++)
+                    ;
+                rle -= i + 1;
+                out.WriteByte(rle);
+            }
+        }
+        out.WriteITF8(F[i]);
+    }
+    out.WriteByte(0);
+}
+function RansEncode0(src) {
+    const nbytes = src.length;
+    var output = new IOStream('', 0, 257 * 3 + 9);
+    output.WriteByte(0); // Order 0
+    output.WriteUint32(0); // compressed size: correct later
+    output.WriteUint32(0); // uncompressed size: correct later
+    // Compute frequencies
+    var F = new Array(256);
+    BuildFrequencies0(src, F);
+    NormaliseFrequencies0(F);
+    WriteFrequencies0(output, F);
+    // Compute cumulative frequencies
+    var C = new Array(256);
+    C[0] = 0;
+    for (var i = 1; i < 256; i++)
+        C[i] = C[i - 1] + F[i - 1];
+    // Initialise rANS state
+    var R = new Array(4);
+    for (var i = 0; i < 4; i++)
+        R[i] = RansEncInit();
+    var alloc = Math.floor(nbytes * 1.05 + 100);
+    var rans_out = new IOStream('', alloc, alloc);
+    // Main encode loop
+    for (var i = nbytes - 1; i >= 0; i--)
+        R[i % 4] = RansEncPut(R[i % 4], rans_out, C[src[i]], F[src[i]], 12);
+    for (var i = 3; i >= 0; i--)
+        RansEncFlush(R[i], rans_out);
+    // Stitch blocks together into final output buffer
+    var freq_tab = output.pos;
+    output.buf.writeInt32LE(freq_tab - 9 + (rans_out.length - rans_out.pos), 1);
+    output.buf.writeInt32LE(nbytes, 5);
+    return Buffer.concat([
+        output.buf.slice(0, output.pos),
+        rans_out.buf.slice(rans_out.pos, rans_out.length),
+    ], output.pos + rans_out.length - rans_out.pos);
+}
+//----------------------------------------------------------------------
+// Order-1 decoder
+// Decode a table of order-1 frequences,
+// filling out the F and C arrays.
+function ReadFrequencies1(src, F, C) {
+    // 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;
+    }
+    var sym = src.ReadByte();
+    var last_sym = sym;
+    var 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
+    var F = new Array(256);
+    var C = new Array(256);
+    ReadFrequencies1(src, F, C);
+    // Fast lookup to avoid slow RansGetSymbolFromFreq
+    var C2S = new Array(256);
+    for (var i = 0; i < 256; i++)
+        C2S[i] = RansBuildC2S(C[i]);
+    // Initialise rANS state
+    var R = new Array(4);
+    var L = new Array(4);
+    for (var j = 0; j < 4; j++) {
+        R[j] = src.ReadUint32();
+        L[j] = 0;
+    }
+    // Main decode loop
+    var output = new Buffer.allocUnsafe(nbytes);
+    var 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;
+}
+//----------------------------------------------------------------------
+// Order-1 encoder
+function BuildFrequencies1(src, F, F0) {
+    for (var i = 0; i < 256; i++) {
+        F0[i] = 0;
+        for (var j = 0; j < 256; j++)
+            F[i][j] = 0;
+    }
+    var last = 0;
+    for (var i = 0; i < src.length; i++) {
+        F0[src[i]]++;
+        F[last][src[i]]++;
+        //F[last][src[i]]++;
+        last = src[i];
+    }
+    // Also accept we'll be starting at 4 points, not just byte 0
+    F[0][src[1 * (src.length >> 2)]]++;
+    F[0][src[2 * (src.length >> 2)]]++;
+    F[0][src[3 * (src.length >> 2)]]++;
+    F0[0] += 3;
+}
+function NormaliseFrequencies1(F, F0) {
+    for (var i = 0; i < 256; i++)
+        if (F0[i])
+            NormaliseFrequencies0(F[i]);
+}
+function WriteFrequencies1(out, F, F0) {
+    var rle = 0;
+    var last_sym = 0;
+    for (var i = 0; i < 256; i++) {
+        if (!F0[i])
+            continue;
+        // Output Symbol if needed and Frequency
+        if (rle > 0)
+            rle--;
+        else {
+            out.WriteByte(i);
+            if (i > 0 && F0[i - 1] > 0) {
+                for (rle = i + 1; rle < 256 && F0[rle]; rle++)
+                    ;
+                rle -= i + 1;
+                out.WriteByte(rle);
+            }
+        }
+        WriteFrequencies0(out, F[i]);
+    }
+    out.WriteByte(0);
+}
+function RansEncode1(src) {
+    const nbytes = src.length;
+    var output = new IOStream('', 0, 257 * 257 * 3 + 9);
+    output.WriteByte(1); // Order 0
+    output.WriteUint32(0); // compressed size: correct later
+    output.WriteUint32(0); // uncompressed size: correct later
+    // Compute frequencies
+    var F0 = new Array(256);
+    var F = new Array(256);
+    var C = new Array(256);
+    for (var i = 0; i < 256; i++) {
+        F[i] = new Array(256);
+        C[i] = new Array(256);
+    }
+    BuildFrequencies1(src, F, F0);
+    NormaliseFrequencies1(F, F0);
+    WriteFrequencies1(output, F, F0);
+    // Compute cumulative frequencies
+    for (var i = 0; i < 256; i++) {
+        if (!F0[i])
+            continue;
+        C[i][0] = 0;
+        for (var j = 1; j < 256; j++)
+            C[i][j] = C[i][j - 1] + F[i][j - 1];
+    }
+    // Initialise rANS state
+    var R = new Array(4);
+    var L = new Array(4);
+    for (var j = 0; j < 4; j++) {
+        R[j] = RansEncInit();
+        L[j] = 0;
+    }
+    var rans_out = new IOStream('', nbytes, nbytes);
+    // We have 4 rans codecs running in parallel on its own 1/4tr of buffer
+    var nbytes4 = Math.floor(nbytes / 4);
+    var idx = new Array(4);
+    var last = new Array(4);
+    for (var j = 0; j < 4; j++) {
+        idx[j] = (j + 1) * nbytes4 - 2;
+        last[j] = src[idx[j] + 1];
+    }
+    // Deal with the remainder if not a multiple of 4
+    last[3] = src[nbytes - 1];
+    for (var i = nbytes - 2; i > 4 * nbytes4 - 2; i--) {
+        R[3] = RansEncPut(R[3], rans_out, C[src[i]][last[3]], F[src[i]][last[3]], 12);
+        last[3] = src[i];
+    }
+    // Main encode loop
+    while (idx[0] >= 0) {
+        for (var j = 3; j >= 0; j--) {
+            var s = src[idx[j]];
+            R[j] = RansEncPut(R[j], rans_out, C[s][last[j]], F[s][last[j]], 12);
+            last[j] = s;
+            idx[j]--;
+        }
+    }
+    for (var j = 3; j >= 0; j--) {
+        R[j] = RansEncPut(R[j], rans_out, C[0][last[j]], F[0][last[j]], 12);
+    }
+    for (var i = 3; i >= 0; i--)
+        RansEncFlush(R[i], rans_out);
+    // Stitch blocks together into final output buffer
+    var freq_tab = output.pos;
+    output.buf.writeInt32LE(freq_tab - 9 + (rans_out.length - rans_out.pos), 1);
+    output.buf.writeInt32LE(nbytes, 5);
+    return Buffer.concat([
+        output.buf.slice(0, output.pos),
+        rans_out.buf.slice(rans_out.pos, rans_out.length),
+    ], output.pos + rans_out.length - rans_out.pos);
+}
+module.exports = { decode, encode };
+//# sourceMappingURL=rans.js.map

package/dist/htscodecs/rans.js.map

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

@@ -0,0 +1,2 @@
+export function decode(src: any): any;
+export function encode(src: any, format: any): Buffer;