@gmod/cram 3.0.6 → 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

@@ -0,0 +1,18 @@
+export = RangeCoderGen;
+declare class RangeCoderGen {
+    decode(src: any): Uint8Array<any>;
+    stream: IOStream | undefined;
+    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)[];
+    decodeStripe(stream: any, len: any): Uint8Array<any>;
+    decodeCat(stream: any, len: any): Uint8Array<any>;
+}
+import IOStream = require("./iostream");

package/dist/htscodecs/arith_gen.js

@@ -0,0 +1,318 @@
+"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 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;
+const ARITH_NOSIZE = 16;
+const ARITH_CAT = 32;
+const ARITH_RLE = 64;
+const ARITH_PACK = 128;
+module.exports = class RangeCoderGen {
+    decode(src) {
+        this.stream = new IOStream(src);
+        return this.decodeStream(this.stream);
+    }
+    decodeStream(stream, n_out = 0) {
+        var flags = this.stream.ReadByte();
+        if (!(flags & ARITH_NOSIZE))
+            n_out = this.stream.ReadUint7();
+        var e_len = n_out;
+        var order = flags & ARITH_ORDER;
+        // 4-way recursion
+        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)
+            var data = this.decodeCat(this.stream, e_len);
+        // Entropy decode
+        else if (flags & ARITH_EXT) {
+            var data = this.decodeExt(this.stream, e_len);
+        }
+        else if (flags & ARITH_RLE) {
+            var data = order
+                ? this.decodeRLE1(this.stream, e_len)
+                : this.decodeRLE0(this.stream, e_len);
+        }
+        else {
+            var data = order
+                ? this.decode1(this.stream, e_len)
+                : this.decode0(this.stream, e_len);
+        }
+        // Transforms
+        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)
+            max_sym = 256;
+        var byte_model = new ByteModel(max_sym);
+        var rc = new RangeCoder(stream);
+        rc.RangeStartDecode(stream);
+        for (var 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)
+            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);
+        rc.RangeStartDecode(stream);
+        var 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);
+        let chunk;
+        const chunks = [];
+        do {
+            chunk = bzip2.decompress(bits, size);
+            if (chunk !== -1) {
+                chunks.push(chunk);
+                size -= chunk.length;
+            }
+        } while (chunk !== -1);
+        return 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)
+            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);
+        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;
+            while (part == 3) {
+                part = model_run[rctx].ModelDecode(stream, rc);
+                rctx = 257;
+                run += part;
+            }
+            for (var 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)
+            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);
+        rc.RangeStartDecode(stream);
+        var 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;
+            while (part == 3) {
+                part = model_run[rctx].ModelDecode(stream, rc);
+                rctx = 257;
+                run += part;
+            }
+            for (var 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++)
+            M[i] = stream.ReadByte();
+        var 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);
+        if (this.nsym <= 1) {
+            // Constant value
+            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)
+                    var v = data[j++];
+                out[i] = M[v & 1];
+                v >>= 1;
+            }
+        }
+        else if (this.nsym <= 4) {
+            // 2 bits per value
+            for (var i = 0, j = 0; i < len; i++) {
+                if (i % 4 == 0)
+                    var v = data[j++];
+                out[i] = M[v & 3];
+                v >>= 2;
+            }
+        }
+        else if (this.nsym <= 16) {
+            // 4 bits per value
+            for (var i = 0, j = 0; i < len; i++) {
+                if (i % 2 == 0)
+                    var v = data[j++];
+                out[i] = M[v & 15];
+                v >>= 4;
+            }
+        }
+        else {
+            // 8 bits per value: NOP
+            return data;
+        }
+        return out;
+    }
+    // Compute M array and return meta-data stream
+    packMeta(src) {
+        var stream = new IOStream('', 0, 1024);
+        // Count symbols
+        var 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
+        stream.WriteByte(nsym);
+        // FIXME: add check for nsym > 16?
+        // Or just accept it as an inefficient waste of time.
+        for (var i = 0; i < 256; i++) {
+            if (M[i]) {
+                stream.WriteByte(i); // adjust to 0..N-1
+                M[i]--;
+            }
+        }
+        return [stream, M, nsym];
+    }
+    decodeStripe(stream, len) {
+        var N = stream.ReadByte();
+        // Retrieve lengths
+        var clen = new Array(N);
+        var ulen = new Array(N);
+        for (var j = 0; j < N; j++)
+            clen[j] = stream.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] = this.decodeStream(stream, 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;
+    }
+    //----------------------------------------------------------------------
+    // Cat method
+    decodeCat(stream, len) {
+        var out = new Uint8Array(len);
+        for (var i = 0; i < len; i++)
+            out[i] = stream.ReadByte();
+        return out;
+    }
+};
+//# sourceMappingURL=arith_gen.js.map

package/dist/htscodecs/arith_gen.js.map

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

@@ -0,0 +1,16 @@
+export = RangeCoder;
+declare 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;
+    RangeShiftLow(dst: any): void;
+    RangeEncode(dst: any, sym_low: any, sym_freq: any, tot_freq: any): void;
+    RangeFinishEncode(dst: any): void;
+}