@gmod/cram 4.0.3 → 4.0.4

package/dist/htscodecs/rans4x16.js

@@ -1,4 +1,11 @@
 "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
@@ -31,8 +38,8 @@
  * (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');
-//----------------------------------------------------------------------
+const iostream_1 = __importDefault(require("./iostream"));
+// ----------------------------------------------------------------------
 // rANS primitives itself
 //
 // RansGet* is decoder side
@@ -43,19 +50,21 @@ 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])
+    let s = 0;
+    while (f >= C[s + 1]) {
         s++;
-    //console.error(f, C, 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])
+    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;
@@ -64,43 +73,47 @@ function RansAdvanceStep(R, c, f, bits) {
     return f * (R >> bits) + (R & ((1 << bits) - 1)) - c;
 }
 function RansRenorm(src, R) {
-    if (R < 1 << 15)
+    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();
+    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 {
-        var comp_meta_len = src.ReadUint7();
+        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);
+        rle_meta = RansDecode0(new iostream_1.default(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)
+    var rle_meta = new iostream_1.default(rle_meta);
+    const L = new Array(256);
+    let n = rle_meta.ReadByte();
+    if (n == 0) {
         n = 256;
-    for (var i = 0; i < n; i++)
+    }
+    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) {
-    var src = new IOStream(buf);
-    var out = new Uint8Array(len);
+    const src = new iostream_1.default(buf);
+    const 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];
+    let j = 0;
+    for (let i = 0; j < len; i++) {
+        const sym = buf[i];
         if (L[sym]) {
-            var run = rle_meta.ReadUint7();
-            for (var r = 0; r <= run; r++)
+            const run = rle_meta.ReadUint7();
+            for (let r = 0; r <= run; r++) {
                 out[j++] = sym;
+            }
         }
         else {
             out[j++] = sym;
@@ -111,28 +124,31 @@ function DecodeRLE(buf, L, rle_meta, len) {
 // 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++)
+    const nsym = src.ReadByte();
+    const P = new Array(nsym);
+    for (let i = 0; i < nsym; i++) {
         P[i] = src.ReadByte();
-    var len = src.ReadUint7();
+    }
+    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) {
-    var out = new Uint8Array(len);
-    var j = 0;
+    const out = new Uint8Array(len);
+    let j = 0;
     // Constant value
     if (nsym <= 1) {
-        for (var i = 0; i < len; i++)
+        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)
+            if (i % 8 == 0) {
                 var v = data[j++];
+            }
             out[i] = P[v & 1];
             v >>= 1;
         }
@@ -140,8 +156,9 @@ function DecodePack(data, P, nsym, len) {
     // 2 bits per value
     else if (nsym <= 4) {
         for (i = 0; i < len; i++) {
-            if (i % 4 == 0)
+            if (i % 4 == 0) {
                 var v = data[j++];
+            }
             out[i] = P[v & 3];
             v >>= 2;
         }
@@ -149,8 +166,9 @@ function DecodePack(data, P, nsym, len) {
     // 4 bits per value
     else if (nsym <= 16) {
         for (i = 0; i < len; i++) {
-            if (i % 2 == 0)
+            if (i % 2 == 0) {
                 var v = data[j++];
+            }
             out[i] = P[v & 15];
             v >>= 4;
         }
@@ -158,49 +176,52 @@ function DecodePack(data, P, nsym, len) {
     return out;
 }
 function RansDecodeStripe(src, len) {
-    var N = src.ReadByte();
+    const N = src.ReadByte();
     // Retrieve lengths
-    var clen = new Array(N);
-    var ulen = new Array(N);
-    for (var j = 0; j < N; j++)
+    const clen = new Array(N);
+    const ulen = new Array(N);
+    for (var j = 0; j < N; j++) {
         clen[j] = src.ReadUint7();
+    }
     // Decode streams
-    var T = new Array(N);
+    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
-    var out = new Uint8Array(len);
+    const out = new Uint8Array(len);
     for (var j = 0; j < N; j++) {
-        for (var i = 0; i < ulen[j]; i++) {
+        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.
 function decode(src) {
-    var stream = new IOStream(src);
+    const stream = new iostream_1.default(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)
+    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)
+    if (stripe) {
         return RansDecodeStripe(stream, n_out);
+    }
     // Bit packing
     if (pack) {
         var pack_len = n_out;
@@ -212,28 +233,34 @@ function RansDecodeStream(stream, n_out) {
         var [L, rle_meta, n_out] = DecodeRLEMeta(stream, Nway);
     }
     // Uncompress data (all, packed or run literals)
-    if (cat)
+    if (cat) {
         var buf = stream.ReadData(n_out);
-    else if (order == 0)
+    }
+    else if (order == 0) {
         var buf = RansDecode0(stream, n_out, Nway);
-    else
+    }
+    else {
         var buf = RansDecode1(stream, n_out, Nway);
+    }
     // Apply expansion transforms
-    if (rle)
+    if (rle) {
         buf = DecodeRLE(buf, L, rle_meta, rle_len);
-    if (pack)
+    }
+    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++)
+    const A = new Array(256);
+    for (let i = 0; i < 256; i++) {
         A[i] = 0;
-    var rle = 0;
-    var sym = src.ReadByte();
-    var last_sym = sym;
+    }
+    let rle = 0;
+    let sym = src.ReadByte();
+    let last_sym = sym;
     do {
         A[sym] = 1;
         if (rle > 0) {
@@ -242,8 +269,9 @@ function ReadAlphabet(src) {
         }
         else {
             sym = src.ReadByte();
-            if (sym == last_sym + 1)
+            if (sym == last_sym + 1) {
                 rle = src.ReadByte();
+            }
         }
         last_sym = sym;
     } while (sym != 0);
@@ -253,38 +281,42 @@ function ReadAlphabet(src) {
 // 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++)
+    for (var i = 0; i < 256; i++) {
         F[i] = 0;
+    }
     // Fetch alphabet
-    var A = ReadAlphabet(src);
+    const A = ReadAlphabet(src);
     // Fetch frequencies for the symbols listed in our alphabet
     for (var i = 0; i < 256; i++) {
-        if (A[i] > 0)
+        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++)
+    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);
+    const F = new Array(256);
+    const C = new Array(256);
     ReadFrequencies0(src, F, C);
     // Fast lookup to avoid slow RansGetSymbolFromFreq
-    var C2S = RansBuildC2S(C, 12);
+    const C2S = RansBuildC2S(C, 12);
     // Initialise rANS state
-    var R = new Array(N);
-    for (var i = 0; i < N; i++)
+    const R = new Array(N);
+    for (var i = 0; i < N; i++) {
         R[i] = src.ReadUint32();
+    }
     // Main decode loop
-    var output = new Uint8Array(nbytes);
+    const 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);
+        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]);
@@ -294,21 +326,24 @@ function RansDecode0(src, nbytes, N) {
 }
 function NormaliseFrequencies0_Shift(F, bits) {
     // Compute total and number of bits to shift by
-    var tot = 0;
-    for (var i = 0; i < 256; i++)
+    let tot = 0;
+    for (var i = 0; i < 256; i++) {
         tot += F[i];
-    if (tot == 0 || tot == 1 << bits)
+    }
+    if (tot == 0 || tot == 1 << bits) {
         return;
-    var shift = 0;
+    }
+    let shift = 0;
     while (tot < 1 << bits) {
         tot *= 2;
         shift++;
     }
     // Scale total of frequencies to (1<<bits)
-    for (var i = 0; i < 256; i++)
+    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.
@@ -317,69 +352,75 @@ function ReadFrequencies1(src, F, C, shift) {
     for (var i = 0; i < 256; i++) {
         F[i] = new Array(256);
         C[i] = new Array(256);
-        for (var j = 0; j < 256; j++)
+        for (var j = 0; j < 256; j++) {
             F[i][j] = 0;
+        }
     }
     // Fetch alphabet
-    var A = ReadAlphabet(src);
+    const A = ReadAlphabet(src);
     // Read F[]
     for (var i = 0; i < 256; i++) {
-        if (!A[i])
+        if (!A[i]) {
             continue;
-        var run = 0;
+        }
+        let run = 0;
         for (var j = 0; j < 256; j++) {
-            if (!A[j])
+            if (!A[j]) {
                 continue;
+            }
             if (run > 0) {
                 run--;
             }
             else {
                 F[i][j] = src.ReadUint7();
-                if (F[i][j] == 0)
+                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++)
+        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;
+    const 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));
+        const ulen = src.ReadUint7();
+        const clen = src.ReadUint7();
+        var comp = new iostream_1.default(src.ReadData(clen));
+        var freq_src = new iostream_1.default(RansDecode0(comp, ulen, 4));
     }
     // Decode frequencies
-    var F = new Array(256);
-    var C = new Array(256);
+    const F = new Array(256);
+    const 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?
+    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
-    var R = new Array(N);
-    var L = new Array(N);
+    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
-    var output = new Uint8Array(nbytes);
-    var nbytesx = Math.floor(nbytes / N);
+    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 = 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);
@@ -401,5 +442,4 @@ function RansDecode1(src, nbytes, N) {
     }
     return output;
 }
-module.exports = { decode };
 //# sourceMappingURL=rans4x16.js.map

package/dist/htscodecs/rans4x16.js.map

@@ -1 +1 @@
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package/dist/htscodecs/tok3.d.ts

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