@gmod/cram 3.0.7 → 4.0.0

package/dist/cramFile/slice/index.js.map

@@ -1 +1 @@
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package/dist/cramFile/util.d.ts

@@ -1,7 +1,7 @@
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
 export declare function parseItf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
-export declare function parseLtf8(buffer: Buffer, initialOffset: number): readonly [number, number];
-export declare function parseItem<T>(buffer: Buffer, parser: (buffer: Buffer, offset: number) => {
+export declare function parseLtf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
+export declare function parseItem<T>(buffer: Uint8Array, parser: (buffer: Uint8Array, offset: number) => {
     offset: number;
     value: T;
 }, startBufferPosition?: number, startFilePosition?: number): T & {
@@ -10,3 +10,5 @@ export declare function parseItem<T>(buffer: Buffer, parser: (buffer: Buffer, of
 };
 export declare function tinyMemoize(_class: any, methodName: any): void;
 export declare function sequenceMD5(seq: string): string;
+export declare function sum(array: Uint8Array[]): number;
+export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;

package/dist/cramFile/util.js

@@ -9,8 +9,10 @@ exports.parseLtf8 = parseLtf8;
 exports.parseItem = parseItem;
 exports.tinyMemoize = tinyMemoize;
 exports.sequenceMD5 = sequenceMD5;
-const md5_1 = __importDefault(require("md5"));
+exports.sum = sum;
+exports.concatUint8Array = concatUint8Array;
 const long_1 = __importDefault(require("long"));
+const md5_1 = __importDefault(require("md5"));
 const getBits_1 = require("./codecs/getBits");
 function itf8Size(v) {
     if (!(v & ~0x7f)) {
@@ -71,6 +73,7 @@ function parseItf8(buffer, initialOffset) {
     return [result, offset - initialOffset];
 }
 function parseLtf8(buffer, initialOffset) {
+    const dataView = new DataView(buffer.buffer);
     let offset = initialOffset;
     const countFlags = buffer[offset];
     let n;
@@ -88,7 +91,7 @@ function parseLtf8(buffer, initialOffset) {
                 (buffer[offset + 1] << 8) |
                 buffer[offset + 2]) &
                 0x1fffff;
-        n = ((countFlags & 63) << 16) | buffer.readUInt16LE(offset + 1);
+        n = ((countFlags & 63) << 16) | dataView.getUint16(offset + 1, true);
         offset += 3;
     }
     else if (countFlags < 0xf0) {
@@ -102,7 +105,7 @@ function parseLtf8(buffer, initialOffset) {
     }
     else if (countFlags < 0xf8) {
         n =
-            ((buffer[offset] & 15) * Math.pow(2, 32) + (buffer[offset + 1] << 24)) |
+            ((buffer[offset] & 15) * 2 ** 32 + (buffer[offset + 1] << 24)) |
                 ((buffer[offset + 2] << 16) |
                     (buffer[offset + 3] << 8) |
                     buffer[offset + 4]);
@@ -111,7 +114,7 @@ function parseLtf8(buffer, initialOffset) {
     }
     else if (countFlags < 0xfc) {
         n =
-            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2, 32) +
+            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * 2 ** 32 +
                 (buffer[offset + 2] << 24)) |
                 ((buffer[offset + 3] << 16) |
                     (buffer[offset + 4] << 8) |
@@ -123,7 +126,7 @@ function parseLtf8(buffer, initialOffset) {
             ((((buffer[offset] & 3) << 16) |
                 (buffer[offset + 1] << 8) |
                 buffer[offset + 2]) *
-                Math.pow(2, 32) +
+                2 ** 32 +
                 (buffer[offset + 3] << 24)) |
                 ((buffer[offset + 4] << 16) |
                     (buffer[offset + 5] << 8) |
@@ -152,7 +155,11 @@ function parseLtf8(buffer, initialOffset) {
 }
 function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
     const { offset, value } = parser(buffer, startBufferPosition);
-    return Object.assign(Object.assign({}, value), { _endPosition: offset + startFilePosition, _size: offset - startBufferPosition });
+    return {
+        ...value,
+        _endPosition: offset + startFilePosition,
+        _size: offset - startBufferPosition,
+    };
 }
 // this would be nice as a decorator, but i'm a little worried about babel
 // support for it going away or changing. memoizes a method in the stupidest
@@ -175,4 +182,20 @@ function tinyMemoize(_class, methodName) {
 function sequenceMD5(seq) {
     return (0, md5_1.default)(seq.toUpperCase().replaceAll(/[^\u0021-\u007e]/g, ''));
 }
+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;
+}
 //# sourceMappingURL=util.js.map

package/dist/cramFile/util.js.map

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

@@ -1,26 +1,18 @@
 export = RangeCoderGen;
 declare class RangeCoderGen {
-    decode(src: any): any;
+    decode(src: any): Uint8Array<any>;
     stream: IOStream | undefined;
-    decodeStream(stream: any, n_out?: number): any;
-    encode(src: any, flags: any): any;
-    decode0(stream: any, n_out: any): any;
-    encode0(src: any, n_in: any, out: any): any;
-    decode1(stream: any, n_out: any): any;
-    encode1(src: any, n_in: any, out: any): any;
-    decodeExt(stream: any, n_out: any): any;
-    encodeExt(stream: any, n_out: any): void;
-    decodeRLE0(stream: any, n_out: any): any;
-    encodeRLE0(src: any, n_in: any, out: any): any;
-    decodeRLE1(stream: any, n_out: any): any;
-    encodeRLE1(src: any, n_in: any, out: any): any;
+    decodeStream(stream: any, n_out?: number): Uint8Array<any>;
+    decode0(stream: any, n_out: any): Uint8Array<any>;
+    decode1(stream: any, n_out: any): Uint8Array<any>;
+    decodeExt(stream: any, n_out: any): Uint8Array<ArrayBuffer>;
+    decodeRLE0(stream: any, n_out: any): Uint8Array<any>;
+    decodeRLE1(stream: any, n_out: any): Uint8Array<any>;
     decodePackMeta(stream: any): any[];
     nsym: any;
     decodePack(data: any, M: any, len: any): any;
     packMeta(src: any): (number | any[] | IOStream)[];
-    encodePack(data: any): any[];
-    encodeStripe(hdr: any, src: any, N: any): any;
-    decodeStripe(stream: any, len: any): any;
-    decodeCat(stream: any, len: any): any;
+    decodeStripe(stream: any, len: any): Uint8Array<any>;
+    decodeCat(stream: any, len: any): Uint8Array<any>;
 }
 import IOStream = require("./iostream");

package/dist/htscodecs/arith_gen.js

@@ -35,6 +35,22 @@ 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 ARITH_ORDER = 1;
 const ARITH_EXT = 4;
 const ARITH_STRIPE = 8;
@@ -83,41 +99,10 @@ module.exports = class RangeCoderGen {
             data = this.decodePack(data, P, n_out);
         return data;
     }
-    encode(src, flags) {
-        this.stream = new IOStream('', 0, src.length * 1.1 + 100); // guestimate worst case!
-        this.stream.WriteByte(flags);
-        if (!(flags & ARITH_NOSIZE))
-            this.stream.WriteUint7(src.length);
-        if (flags & ARITH_STRIPE)
-            return Buffer.concat([
-                this.stream.buf.slice(0, this.stream.pos),
-                this.encodeStripe(this.stream, src, flags >> 8),
-            ]);
-        var order = flags & ARITH_ORDER;
-        var e_len = src.length;
-        // step 1: Encode meta-data
-        var pack_meta;
-        if (flags & ARITH_PACK)
-            [pack_meta, src, e_len] = this.encodePack(src);
-        // step 2: Write any meta data
-        if (flags & ARITH_PACK)
-            this.stream.WriteStream(pack_meta);
-        // step 3: arith encoding below
-        if (flags & ARITH_RLE) {
-            return order
-                ? this.encodeRLE1(src, e_len, this.stream)
-                : this.encodeRLE0(src, e_len, this.stream);
-        }
-        else {
-            return order
-                ? this.encode1(src, e_len, this.stream)
-                : this.encode0(src, e_len, this.stream);
-        }
-    }
     //----------------------------------------------------------------------
     // Order-0 codec
     decode0(stream, n_out) {
-        var output = new Buffer.allocUnsafe(n_out);
+        var output = new Uint8Array(n_out);
         var max_sym = stream.ReadByte();
         if (max_sym == 0)
             max_sym = 256;
@@ -128,25 +113,10 @@ module.exports = class RangeCoderGen {
             output[i] = byte_model.ModelDecode(stream, rc);
         return output;
     }
-    encode0(src, n_in, out) {
-        // Count the maximum symbol present
-        var max_sym = 0;
-        for (var i = 0; i < n_in; i++)
-            if (max_sym < src[i])
-                max_sym = src[i];
-        max_sym++; // FIXME not what spec states!?
-        var byte_model = new ByteModel(max_sym);
-        out.WriteByte(max_sym);
-        var rc = new RangeCoder(out);
-        for (var i = 0; i < n_in; i++)
-            byte_model.ModelEncode(out, rc, src[i]);
-        rc.RangeFinishEncode(out);
-        return out.buf.slice(0, out.pos);
-    }
     //----------------------------------------------------------------------
     // Order-1 codec
     decode1(stream, n_out) {
-        var output = new Buffer.allocUnsafe(n_out);
+        var output = new Uint8Array(n_out);
         var max_sym = stream.ReadByte();
         if (max_sym == 0)
             max_sym = 256;
@@ -162,53 +132,26 @@ module.exports = class RangeCoderGen {
         }
         return output;
     }
-    encode1(src, n_in, out) {
-        // Count the maximum symbol present
-        var max_sym = 0;
-        for (var i = 0; i < n_in; i++)
-            if (max_sym < src[i])
-                max_sym = src[i];
-        max_sym++; // FIXME not what spec states!
-        var byte_model = new Array(max_sym);
-        for (var i = 0; i < max_sym; i++)
-            byte_model[i] = new ByteModel(max_sym);
-        out.WriteByte(max_sym);
-        var rc = new RangeCoder(out);
-        var last = 0;
-        for (var i = 0; i < n_in; i++) {
-            byte_model[last].ModelEncode(out, rc, src[i]);
-            last = src[i];
-        }
-        rc.RangeFinishEncode(out);
-        return out.buf.slice(0, out.pos);
-    }
     //----------------------------------------------------------------------
     // External codec
     decodeExt(stream, n_out) {
-        // Bzip2 only for now
-        var output = new Buffer.allocUnsafe(n_out);
-        var bits = bzip2.array(stream.buf.slice(stream.pos));
-        var size = bzip2.header(bits);
-        var j = 0;
+        const bits = bzip2.array(stream.buf.slice(stream.pos));
+        let size = bzip2.header(bits);
+        let chunk;
+        const chunks = [];
         do {
-            var chunk = bzip2.decompress(bits, size);
-            if (chunk != -1) {
-                Buffer.from(chunk).copy(output, j);
-                j += chunk.length;
+            chunk = bzip2.decompress(bits, size);
+            if (chunk !== -1) {
+                chunks.push(chunk);
                 size -= chunk.length;
             }
-        } while (chunk != -1);
-        return output;
-    }
-    encodeExt(stream, n_out) {
-        // We cannot compress using Bzip2 now as it's
-        // absent from bzip2.js, but consider using
-        // https://github.com/cscott/compressjs
+        } while (chunk !== -1);
+        return concatUint8Array(chunks);
     }
     //----------------------------------------------------------------------
     // Order-0 RLE codec
     decodeRLE0(stream, n_out) {
-        var output = new Buffer.allocUnsafe(n_out);
+        var output = new Uint8Array(n_out);
         var max_sym = stream.ReadByte();
         if (max_sym == 0)
             max_sym = 256;
@@ -235,47 +178,10 @@ module.exports = class RangeCoderGen {
         }
         return output;
     }
-    encodeRLE0(src, n_in, out) {
-        // Count the maximum symbol present
-        var max_sym = 0;
-        for (var i = 0; i < n_in; i++)
-            if (max_sym < src[i])
-                max_sym = src[i];
-        max_sym++; // FIXME not what spec states!
-        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);
-        out.WriteByte(max_sym);
-        var rc = new RangeCoder(out);
-        var i = 0;
-        while (i < n_in) {
-            model_lit.ModelEncode(out, rc, src[i]);
-            var run = 1;
-            while (i + run < n_in && src[i + run] == src[i])
-                run++;
-            run--;
-            var rctx = src[i];
-            var last = src[i];
-            i += run + 1;
-            var part = run >= 3 ? 3 : run;
-            model_run[rctx].ModelEncode(out, rc, part);
-            run -= part;
-            rctx = 256;
-            while (part == 3) {
-                part = run >= 3 ? 3 : run;
-                model_run[rctx].ModelEncode(out, rc, part);
-                rctx = 257;
-                run -= part;
-            }
-        }
-        rc.RangeFinishEncode(out);
-        return out.buf.slice(0, out.pos);
-    }
     //----------------------------------------------------------------------
     // Order-1 RLE codec
     decodeRLE1(stream, n_out) {
-        var output = new Buffer.allocUnsafe(n_out);
+        var output = new Uint8Array(n_out);
         var max_sym = stream.ReadByte();
         if (max_sym == 0)
             max_sym = 256;
@@ -306,46 +212,6 @@ module.exports = class RangeCoderGen {
         }
         return output;
     }
-    encodeRLE1(src, n_in, out) {
-        // Count the maximum symbol present
-        var max_sym = 0;
-        for (var i = 0; i < n_in; i++)
-            if (max_sym < src[i])
-                max_sym = src[i];
-        max_sym++; // FIXME not what spec states!
-        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);
-        out.WriteByte(max_sym);
-        var rc = new RangeCoder(out);
-        var i = 0;
-        var last = 0;
-        while (i < n_in) {
-            model_lit[last].ModelEncode(out, rc, src[i]);
-            var run = 1;
-            while (i + run < n_in && src[i + run] == src[i])
-                run++;
-            run--;
-            var rctx = src[i];
-            last = src[i];
-            i += run + 1;
-            var part = run >= 3 ? 3 : run;
-            model_run[rctx].ModelEncode(out, rc, part);
-            run -= part;
-            rctx = 256;
-            while (part == 3) {
-                part = run >= 3 ? 3 : run;
-                model_run[rctx].ModelEncode(out, rc, part);
-                rctx = 257;
-                run -= part;
-            }
-        }
-        rc.RangeFinishEncode(out);
-        return out.buf.slice(0, out.pos);
-    }
     //----------------------------------------------------------------------
     // Pack method
     decodePackMeta(stream) {
@@ -357,7 +223,7 @@ module.exports = class RangeCoderGen {
         return [M, e_len];
     }
     decodePack(data, M, len) {
-        var out = new Buffer.allocUnsafe(len);
+        var out = new Uint8Array(len);
         if (this.nsym <= 1) {
             // Constant value
             for (var i = 0; i < len; i++)
@@ -418,112 +284,6 @@ module.exports = class RangeCoderGen {
         }
         return [stream, M, nsym];
     }
-    encodePack(data) {
-        var meta, M, nsym;
-        [meta, M, nsym] = this.packMeta(data);
-        var len = data.length;
-        var i = 0;
-        if (nsym <= 1) {
-            // Constant values
-            meta.WriteUint7(0);
-            return [meta, new Buffer.allocUnsafe(0), 0];
-        }
-        if (nsym <= 2) {
-            // 1 bit per value
-            var out = new Buffer.allocUnsafe(Math.floor((len + 7) / 8));
-            for (var i = 0, j = 0; i < (len & ~7); i += 8, j++)
-                out[j] =
-                    (M[data[i + 0]] << 0) +
-                        (M[data[i + 1]] << 1) +
-                        (M[data[i + 2]] << 2) +
-                        (M[data[i + 3]] << 3) +
-                        (M[data[i + 4]] << 4) +
-                        (M[data[i + 5]] << 5) +
-                        (M[data[i + 6]] << 6) +
-                        (M[data[i + 7]] << 7);
-            if (i < len) {
-                out[j] = 0;
-                var v = 0;
-                while (i < len) {
-                    out[j] |= M[data[i++]] << v;
-                    v++;
-                }
-                j++;
-            }
-            meta.WriteUint7(j);
-            return [meta, out, out.length];
-        }
-        if (nsym <= 4) {
-            // 2 bits per value
-            var out = new Buffer.allocUnsafe(Math.floor((len + 3) / 4));
-            for (var i = 0, j = 0; i < (len & ~3); i += 4, j++)
-                out[j] =
-                    (M[data[i + 0]] << 0) +
-                        (M[data[i + 1]] << 2) +
-                        (M[data[i + 2]] << 4) +
-                        (M[data[i + 3]] << 6);
-            if (i < len) {
-                out[j] = 0;
-                var v = 0;
-                while (i < len) {
-                    out[j] |= M[data[i++]] << v;
-                    v += 2;
-                }
-                j++;
-            }
-            meta.WriteUint7(j);
-            return [meta, out, out.length];
-        }
-        if (nsym <= 16) {
-            // 4 bits per value
-            var out = new Buffer.allocUnsafe(Math.floor((len + 1) / 2));
-            for (var i = 0, j = 0; i < (len & ~1); i += 2, j++)
-                out[j] = (M[data[i + 0]] << 0) + (M[data[i + 1]] << 4);
-            if (i < len)
-                out[j++] = M[data[i++]];
-            meta.WriteUint7(j);
-            return [meta, out, out.length];
-        }
-        // Otherwise an expensive NOP
-        meta.WriteUint7(data.length);
-        return [meta, data, data.length];
-    }
-    //----------------------------------------------------------------------
-    // STRIPE method
-    encodeStripe(hdr, src, N) {
-        if (N == 0)
-            N = 4; // old default
-        // Split into multiple streams
-        var part = new Array(N);
-        var ulen = new Array(N);
-        for (var s = 0; s < N; s++) {
-            ulen[s] = Math.floor(src.length / N) + (src.length % N > s);
-            part[s] = new Array(ulen[s]);
-        }
-        for (var x = 0, i = 0; i < src.length; i += N, x++) {
-            for (var j = 0; j < N; j++)
-                if (x < part[j].length)
-                    part[j][x] = src[i + j];
-        }
-        // Compress each part
-        var comp = new Array(N);
-        var total = 0;
-        for (var s = 0; s < N; s++) {
-            // Example: try O0 and O1 and choose best
-            var comp0 = this.encode(part[s], 0);
-            var comp1 = this.encode(part[s], 1);
-            comp[s] = comp1.length < comp0.length ? comp1 : comp0;
-            total += comp[s].length;
-        }
-        // Serialise
-        var out = new IOStream('', 0, total + 5 * N + 1);
-        out.WriteByte(N);
-        for (var s = 0; s < N; s++)
-            out.WriteUint7(comp[s].length);
-        for (var s = 0; s < N; s++)
-            out.WriteData(comp[s], comp[s].length);
-        return out.buf.slice(0, out.buf.pos);
-    }
     decodeStripe(stream, len) {
         var N = stream.ReadByte();
         // Retrieve lengths
@@ -538,7 +298,7 @@ module.exports = class RangeCoderGen {
             T[j] = this.decodeStream(stream, ulen[j]);
         }
         // Transpose
-        var out = new Buffer.allocUnsafe(len);
+        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];
@@ -549,7 +309,7 @@ module.exports = class RangeCoderGen {
     //----------------------------------------------------------------------
     // Cat method
     decodeCat(stream, len) {
-        var out = new Buffer.allocUnsafe(len);
+        var out = new Uint8Array(len);
         for (var i = 0; i < len; i++)
             out[i] = stream.ReadByte();
         return out;