@gmod/cram 4.0.3 → 4.0.4

package/dist/htscodecs/arith_gen.js

@@ -1,4 +1,10 @@
 "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 });
 /*
  * Copyright (c) 2019,2020 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -31,26 +37,11 @@
  * (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 RangeCoder = require('./arith_sh');
-const IOStream = require('./iostream');
-const ByteModel = require('./byte_model');
-const bzip2 = require('bzip2');
-function sum(array) {
-    let sum = 0;
-    for (const entry of array) {
-        sum += entry.length;
-    }
-    return sum;
-}
-function concatUint8Array(args) {
-    const mergedArray = new Uint8Array(sum(args));
-    let offset = 0;
-    for (const entry of args) {
-        mergedArray.set(entry, offset);
-        offset += entry.length;
-    }
-    return mergedArray;
-}
+const bzip2_1 = __importDefault(require("bzip2"));
+const arith_sh_1 = __importDefault(require("./arith_sh"));
+const byte_model_1 = __importDefault(require("./byte_model"));
+const iostream_1 = __importDefault(require("./iostream"));
+const util_1 = require("../util");
 const ARITH_ORDER = 1;
 const ARITH_EXT = 4;
 const ARITH_STRIPE = 8;
@@ -58,28 +49,31 @@ const ARITH_NOSIZE = 16;
 const ARITH_CAT = 32;
 const ARITH_RLE = 64;
 const ARITH_PACK = 128;
-module.exports = class RangeCoderGen {
+class RangeCoderGen {
     decode(src) {
-        this.stream = new IOStream(src);
+        this.stream = new iostream_1.default(src);
         return this.decodeStream(this.stream);
     }
     decodeStream(stream, n_out = 0) {
-        var flags = this.stream.ReadByte();
-        if (!(flags & ARITH_NOSIZE))
+        const flags = this.stream.ReadByte();
+        if (!(flags & ARITH_NOSIZE)) {
             n_out = this.stream.ReadUint7();
-        var e_len = n_out;
-        var order = flags & ARITH_ORDER;
+        }
+        let e_len = n_out;
+        const order = flags & ARITH_ORDER;
         // 4-way recursion
-        if (flags & ARITH_STRIPE)
+        if (flags & ARITH_STRIPE) {
             return this.decodeStripe(this.stream, n_out);
+        }
         // Meta data
         if (flags & ARITH_PACK) {
             var P;
             [P, e_len] = this.decodePackMeta(this.stream);
         }
         // NOP, useful for tiny blocks
-        if (flags & ARITH_CAT)
+        if (flags & ARITH_CAT) {
             var data = this.decodeCat(this.stream, e_len);
+        }
         // Entropy decode
         else if (flags & ARITH_EXT) {
             var data = this.decodeExt(this.stream, e_len);
@@ -95,145 +89,160 @@ module.exports = class RangeCoderGen {
                 : this.decode0(this.stream, e_len);
         }
         // Transforms
-        if (flags & ARITH_PACK)
+        if (flags & ARITH_PACK) {
             data = this.decodePack(data, P, n_out);
+        }
         return data;
     }
-    //----------------------------------------------------------------------
+    // ----------------------------------------------------------------------
     // Order-0 codec
     decode0(stream, n_out) {
-        var output = new Uint8Array(n_out);
-        var max_sym = stream.ReadByte();
-        if (max_sym == 0)
+        const output = new Uint8Array(n_out);
+        let max_sym = stream.ReadByte();
+        if (max_sym == 0) {
             max_sym = 256;
-        var byte_model = new ByteModel(max_sym);
-        var rc = new RangeCoder(stream);
+        }
+        const byte_model = new byte_model_1.default(max_sym);
+        const rc = new arith_sh_1.default(stream);
         rc.RangeStartDecode(stream);
-        for (var i = 0; i < n_out; i++)
+        for (let i = 0; i < n_out; i++) {
             output[i] = byte_model.ModelDecode(stream, rc);
+        }
         return output;
     }
-    //----------------------------------------------------------------------
+    // ----------------------------------------------------------------------
     // Order-1 codec
     decode1(stream, n_out) {
-        var output = new Uint8Array(n_out);
-        var max_sym = stream.ReadByte();
-        if (max_sym == 0)
+        const output = new Uint8Array(n_out);
+        let max_sym = stream.ReadByte();
+        if (max_sym == 0) {
             max_sym = 256;
-        var byte_model = new Array(max_sym);
-        for (var i = 0; i < max_sym; i++)
-            byte_model[i] = new ByteModel(max_sym);
-        var rc = new RangeCoder(stream);
+        }
+        const byte_model = new Array(max_sym);
+        for (var i = 0; i < max_sym; i++) {
+            byte_model[i] = new byte_model_1.default(max_sym);
+        }
+        const rc = new arith_sh_1.default(stream);
         rc.RangeStartDecode(stream);
-        var last = 0;
+        let last = 0;
         for (var i = 0; i < n_out; i++) {
             output[i] = byte_model[last].ModelDecode(stream, rc);
             last = output[i];
         }
         return output;
     }
-    //----------------------------------------------------------------------
+    // ----------------------------------------------------------------------
     // External codec
     decodeExt(stream, n_out) {
-        const bits = bzip2.array(stream.buf.slice(stream.pos));
-        let size = bzip2.header(bits);
+        const bits = bzip2_1.default.array(stream.buf.slice(stream.pos));
+        let size = bzip2_1.default.header(bits);
         let chunk;
         const chunks = [];
         do {
-            chunk = bzip2.decompress(bits, size);
+            chunk = bzip2_1.default.decompress(bits, size);
             if (chunk !== -1) {
                 chunks.push(chunk);
                 size -= chunk.length;
             }
         } while (chunk !== -1);
-        return concatUint8Array(chunks);
+        return (0, util_1.concatUint8Array)(chunks);
     }
-    //----------------------------------------------------------------------
+    // ----------------------------------------------------------------------
     // Order-0 RLE codec
     decodeRLE0(stream, n_out) {
-        var output = new Uint8Array(n_out);
-        var max_sym = stream.ReadByte();
-        if (max_sym == 0)
+        const output = new Uint8Array(n_out);
+        let max_sym = stream.ReadByte();
+        if (max_sym == 0) {
             max_sym = 256;
-        var model_lit = new ByteModel(max_sym);
-        var model_run = new Array(258);
-        for (var i = 0; i <= 257; i++)
-            model_run[i] = new ByteModel(4);
-        var rc = new RangeCoder(stream);
+        }
+        const model_lit = new byte_model_1.default(max_sym);
+        const model_run = new Array(258);
+        for (var i = 0; i <= 257; i++) {
+            model_run[i] = new byte_model_1.default(4);
+        }
+        const rc = new arith_sh_1.default(stream);
         rc.RangeStartDecode(stream);
         var i = 0;
         while (i < n_out) {
             output[i] = model_lit.ModelDecode(stream, rc);
-            var part = model_run[output[i]].ModelDecode(stream, rc);
-            var run = part;
-            var rctx = 256;
+            let part = model_run[output[i]].ModelDecode(stream, rc);
+            let run = part;
+            let rctx = 256;
             while (part == 3) {
                 part = model_run[rctx].ModelDecode(stream, rc);
                 rctx = 257;
                 run += part;
             }
-            for (var j = 1; j <= run; j++)
+            for (let j = 1; j <= run; j++) {
                 output[i + j] = output[i];
+            }
             i += run + 1;
         }
         return output;
     }
-    //----------------------------------------------------------------------
+    // ----------------------------------------------------------------------
     // Order-1 RLE codec
     decodeRLE1(stream, n_out) {
-        var output = new Uint8Array(n_out);
-        var max_sym = stream.ReadByte();
-        if (max_sym == 0)
+        const output = new Uint8Array(n_out);
+        let max_sym = stream.ReadByte();
+        if (max_sym == 0) {
             max_sym = 256;
-        var model_lit = new Array(max_sym);
-        for (var i = 0; i < max_sym; i++)
-            model_lit[i] = new ByteModel(max_sym);
-        var model_run = new Array(258);
-        for (var i = 0; i <= 257; i++)
-            model_run[i] = new ByteModel(4);
-        var rc = new RangeCoder(stream);
+        }
+        const model_lit = new Array(max_sym);
+        for (var i = 0; i < max_sym; i++) {
+            model_lit[i] = new byte_model_1.default(max_sym);
+        }
+        const model_run = new Array(258);
+        for (var i = 0; i <= 257; i++) {
+            model_run[i] = new byte_model_1.default(4);
+        }
+        const rc = new arith_sh_1.default(stream);
         rc.RangeStartDecode(stream);
-        var last = 0;
+        let last = 0;
         var i = 0;
         while (i < n_out) {
             output[i] = model_lit[last].ModelDecode(stream, rc);
             last = output[i];
-            var part = model_run[output[i]].ModelDecode(stream, rc);
-            var run = part;
-            var rctx = 256;
+            let part = model_run[output[i]].ModelDecode(stream, rc);
+            let run = part;
+            let rctx = 256;
             while (part == 3) {
                 part = model_run[rctx].ModelDecode(stream, rc);
                 rctx = 257;
                 run += part;
             }
-            for (var j = 1; j <= run; j++)
+            for (let j = 1; j <= run; j++) {
                 output[i + j] = output[i];
+            }
             i += run + 1;
         }
         return output;
     }
-    //----------------------------------------------------------------------
+    // ----------------------------------------------------------------------
     // Pack method
     decodePackMeta(stream) {
         this.nsym = stream.ReadByte();
-        var M = new Array(this.nsym);
-        for (var i = 0; i < this.nsym; i++)
+        const M = new Array(this.nsym);
+        for (let i = 0; i < this.nsym; i++) {
             M[i] = stream.ReadByte();
-        var e_len = stream.ReadUint7(); // Could be derived data from nsym and n_out
+        }
+        const e_len = stream.ReadUint7(); // Could be derived data from nsym and n_out
         return [M, e_len];
     }
     decodePack(data, M, len) {
-        var out = new Uint8Array(len);
+        const out = new Uint8Array(len);
         if (this.nsym <= 1) {
             // Constant value
-            for (var i = 0; i < len; i++)
+            for (var i = 0; i < len; i++) {
                 out[i] = M[0];
+            }
         }
         else if (this.nsym <= 2) {
             // 1 bit per value
             for (var i = 0, j = 0; i < len; i++) {
-                if (i % 8 == 0)
+                if (i % 8 == 0) {
                     var v = data[j++];
+                }
                 out[i] = M[v & 1];
                 v >>= 1;
             }
@@ -241,8 +250,9 @@ module.exports = class RangeCoderGen {
         else if (this.nsym <= 4) {
             // 2 bits per value
             for (var i = 0, j = 0; i < len; i++) {
-                if (i % 4 == 0)
+                if (i % 4 == 0) {
                     var v = data[j++];
+                }
                 out[i] = M[v & 3];
                 v >>= 2;
             }
@@ -250,8 +260,9 @@ module.exports = class RangeCoderGen {
         else if (this.nsym <= 16) {
             // 4 bits per value
             for (var i = 0, j = 0; i < len; i++) {
-                if (i % 2 == 0)
+                if (i % 2 == 0) {
                     var v = data[j++];
+                }
                 out[i] = M[v & 15];
                 v >>= 4;
             }
@@ -264,15 +275,18 @@ module.exports = class RangeCoderGen {
     }
     // Compute M array and return meta-data stream
     packMeta(src) {
-        var stream = new IOStream('', 0, 1024);
+        const stream = new iostream_1.default('', 0, 1024);
         // Count symbols
-        var M = new Array(256);
-        for (var i = 0; i < src.length; i++)
+        const M = new Array(256);
+        for (var i = 0; i < src.length; i++) {
             M[src[i]] = 1;
+        }
         // Write Map
-        for (var nsym = 0, i = 0; i < 256; i++)
-            if (M[i])
-                M[i] = ++nsym; // map to 1..N
+        for (var nsym = 0, i = 0; i < 256; i++) {
+            if (M[i]) {
+                M[i] = ++nsym;
+            }
+        } // map to 1..N
         stream.WriteByte(nsym);
         // FIXME: add check for nsym > 16?
         // Or just accept it as an inefficient waste of time.
@@ -285,34 +299,37 @@ module.exports = class RangeCoderGen {
         return [stream, M, nsym];
     }
     decodeStripe(stream, len) {
-        var N = stream.ReadByte();
+        const N = stream.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] = stream.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] = this.decodeStream(stream, 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;
     }
-    //----------------------------------------------------------------------
+    // ----------------------------------------------------------------------
     // Cat method
     decodeCat(stream, len) {
-        var out = new Uint8Array(len);
-        for (var i = 0; i < len; i++)
+        const out = new Uint8Array(len);
+        for (let i = 0; i < len; i++) {
             out[i] = stream.ReadByte();
+        }
         return out;
     }
-};
+}
+exports.default = RangeCoderGen;
 //# sourceMappingURL=arith_gen.js.map

package/dist/htscodecs/arith_gen.js.map

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

@@ -1,12 +1,5 @@
-export = RangeCoder;
-declare class RangeCoder {
+export default class RangeCoder {
     constructor(src: any);
-    low: number;
-    range: number;
-    code: number;
-    FFnum: number;
-    carry: number;
-    cache: number;
     RangeStartDecode(src: any): void;
     RangeGetFrequency(tot_freq: any): number;
     RangeDecode(src: any, sym_low: any, sym_freq: any, tot_freq: any): void;

package/dist/htscodecs/arith_sh.js

@@ -1,4 +1,6 @@
 "use strict";
+// @ts-nocheck
+Object.defineProperty(exports, "__esModule", { value: true });
 /*
  * Copyright (c) 2019 Genome Research Ltd.
  * Author(s): James Bonfield
@@ -38,9 +40,9 @@
 // C:              3.1s decode  (approx same vs 32-bit and 64-bit)
 // Arith_sh.js     6.7s decode  (32-bit with carries)
 // Arith.js      317.0s decode  (64-bit no carries); int64 crippling it.
-//----------------------------------------------------------------------
+// ----------------------------------------------------------------------
 // Arithmetic (range) coder
-module.exports = class RangeCoder {
+class RangeCoder {
     constructor(src) {
         this.low = 0;
         this.range = 0xffffffff;
@@ -50,21 +52,22 @@ module.exports = class RangeCoder {
         this.cache = 0;
     }
     RangeStartDecode(src) {
-        for (var i = 0; i < 5; i++)
+        for (let i = 0; i < 5; i++) {
             this.code = (this.code << 8) + src.ReadByte();
+        }
         this.code &= 0xffffffff;
         this.code >>>= 0; // force to be +ve int
     }
     RangeGetFrequency(tot_freq) {
         this.range = Math.floor(this.range / tot_freq);
-        //return this.code / this.range;
+        // return this.code / this.range;
         return Math.floor(this.code / this.range);
         // Conceptual scenario; return freq only and don't modify range yet
-        //return Math.floor(this.code / (Math.floor(this.range / tot_freq)));
+        // return Math.floor(this.code / (Math.floor(this.range / tot_freq)));
     }
     RangeDecode(src, sym_low, sym_freq, tot_freq) {
         // Conceptually we divide range here, but in practice we cached it earlier
-        //this.range = Math.floor(this.range / tot_freq);
+        // this.range = Math.floor(this.range / tot_freq);
         this.code -= sym_low * this.range;
         this.range *= sym_freq;
         while (this.range < 1 << 24) {
@@ -101,7 +104,7 @@ module.exports = class RangeCoder {
         this.low >>>= 0; // force to be +ve int
     }
     RangeEncode(dst, sym_low, sym_freq, tot_freq) {
-        var old_low = this.low;
+        const old_low = this.low;
         this.range = Math.floor(this.range / tot_freq);
         this.low += sym_low * this.range;
         this.low >>>= 0; // Truncate to +ve int so we can spot overflow
@@ -110,8 +113,9 @@ module.exports = class RangeCoder {
         // NB: can this.low < old_low occur twice before range < (1<<24)?
         // We claim not, but prove it!
         if (this.low < old_low) {
-            if (this.carry != 0)
+            if (this.carry != 0) {
                 console.log('ERROR: Multiple carry');
+            }
             this.carry = 1;
         }
         // Renormalise if range gets too small
@@ -121,8 +125,10 @@ module.exports = class RangeCoder {
         }
     }
     RangeFinishEncode(dst) {
-        for (var i = 0; i < 5; i++)
+        for (let i = 0; i < 5; i++) {
             this.RangeShiftLow(dst);
+        }
     }
-};
+}
+exports.default = RangeCoder;
 //# sourceMappingURL=arith_sh.js.map

package/dist/htscodecs/arith_sh.js.map

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

@@ -1,10 +1,5 @@
-export = ByteModel;
-declare class ByteModel {
+export default class ByteModel {
     constructor(max_sym?: number);
-    total_freq: number;
-    max_sym: number;
-    S: any[];
-    F: any[];
     ModelDecode(src: any, rc: any): any;
     ModelRenormalise(): void;
     ModelEncode(dst: any, rc: any, sym: any): void;