@gmod/cram 3.0.5 → 3.0.7

package/esm/cramFile/util.js.map

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

@@ -0,0 +1,26 @@
+export = RangeCoderGen;
+declare class RangeCoderGen {
+    decode(src: any): 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;
+    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;
+}
+import IOStream = require("./iostream");

package/esm/htscodecs/arith_gen.js

@@ -0,0 +1,558 @@
+"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');
+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;
+    }
+    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 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;
+    }
+    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 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;
+    }
+    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;
+        do {
+            var chunk = bzip2.decompress(bits, size);
+            if (chunk != -1) {
+                Buffer.from(chunk).copy(output, j);
+                j += chunk.length;
+                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
+    }
+    //----------------------------------------------------------------------
+    // Order-0 RLE codec
+    decodeRLE0(stream, n_out) {
+        var output = new Buffer.allocUnsafe(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;
+    }
+    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 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;
+    }
+    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) {
+        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 Buffer.allocUnsafe(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];
+    }
+    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
+        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 Buffer.allocUnsafe(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 Buffer.allocUnsafe(len);
+        for (var i = 0; i < len; i++)
+            out[i] = stream.ReadByte();
+        return out;
+    }
+};
+//# sourceMappingURL=arith_gen.js.map

package/esm/htscodecs/arith_gen.js.map

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package/esm/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;
+}