@gmod/cram 3.0.6 → 4.0.0

package/dist/htscodecs/index.js

@@ -0,0 +1,70 @@
+"use strict";
+/*
+ * Copyright (c) 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.
+ */
+// This is an interface to the htscodecs reference implementation of
+// the CRAM 3.1 codecs.
+// This JavaScript file is not part of the reference implementation
+// and is simply and interface to get a consistent interface for cram-js.
+var r4x8 = require('./rans');
+var r4x16 = require('./rans4x16');
+var arith = require('./arith_gen');
+var fqzcomp = require('./fqzcomp');
+var tok3 = require('./tok3');
+function r4x8_uncompress(inputBuffer, outputBuffer) {
+    return r4x8.decode(inputBuffer);
+}
+function r4x16_uncompress(inputBuffer) {
+    return r4x16.decode(inputBuffer);
+}
+function arith_uncompress(inputBuffer) {
+    // fix by @cmdcolin for CRAM 3.1
+    // xref https://github.com/jkbonfield/htscodecs/pull/1/files
+    return new arith().decode(inputBuffer);
+}
+function fqzcomp_uncompress(inputBuffer) {
+    var q_lens = new Array();
+    return fqzcomp.decode(inputBuffer, q_lens);
+}
+function tok3_uncompress(inputBuffer) {
+    // Returns in string form instead of buffer
+    var out = tok3.decode(inputBuffer, 0, '\0');
+    return Uint8Array.from(Array.from(out).map(letter => letter.charCodeAt(0)));
+}
+module.exports = {
+    r4x8_uncompress: r4x8_uncompress,
+    r4x16_uncompress: r4x16_uncompress,
+    arith_uncompress: arith_uncompress,
+    fqzcomp_uncompress: fqzcomp_uncompress,
+    tok3_uncompress: tok3_uncompress,
+};
+//# sourceMappingURL=index.js.map

package/dist/htscodecs/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/htscodecs/index.js"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,oEAAoE;AACpE,uBAAuB;AAEvB,mEAAmE;AACnE,yEAAyE;AAEzE,IAAI,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;AAC5B,IAAI,KAAK,GAAG,OAAO,CAAC,YAAY,CAAC,CAAA;AACjC,IAAI,KAAK,GAAG,OAAO,CAAC,aAAa,CAAC,CAAA;AAClC,IAAI,OAAO,GAAG,OAAO,CAAC,WAAW,CAAC,CAAA;AAClC,IAAI,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;AAE5B,SAAS,eAAe,CAAC,WAAW,EAAE,YAAY;IAChD,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACjC,CAAC;AAED,SAAS,gBAAgB,CAAC,WAAW;IACnC,OAAO,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AAClC,CAAC;AAED,SAAS,gBAAgB,CAAC,WAAW;IACnC,gCAAgC;IAChC,4DAA4D;IAC5D,OAAO,IAAI,KAAK,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACxC,CAAC;AAED,SAAS,kBAAkB,CAAC,WAAW;IACrC,IAAI,MAAM,GAAG,IAAI,KAAK,EAAE,CAAA;IACxB,OAAO,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,CAAA;AAC5C,CAAC;AAED,SAAS,eAAe,CAAC,WAAW;IAClC,2CAA2C;IAC3C,IAAI,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAC3C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC7E,CAAC;AAED,MAAM,CAAC,OAAO,GAAG;IACf,eAAe,EAAE,eAAe;IAChC,gBAAgB,EAAE,gBAAgB;IAClC,gBAAgB,EAAE,gBAAgB;IAClC,kBAAkB,EAAE,kBAAkB;IACtC,eAAe,EAAE,eAAe;CACjC,CAAA"}

package/dist/htscodecs/iostream.d.ts

@@ -0,0 +1,27 @@
+export = IOStream;
+declare class IOStream {
+    constructor(buf: any, start_pos?: number, size?: number);
+    buf: any;
+    length: any;
+    dataView: DataView<any>;
+    pos: number;
+    EOF(): boolean;
+    ReadData(len: any): any;
+    ReadByte(): any;
+    ReadChar(): string;
+    ReadUint16(): any;
+    ReadUint32(): number;
+    ReadString(): string;
+    ReadUint7(): number;
+    ReadITF8(): any;
+    WriteByte(b: any): void;
+    WriteChar(b: any): void;
+    WriteString(str: any): void;
+    WriteData(buf: any, len: any): void;
+    WriteStream(stream: any): void;
+    WriteUint16(u: any): void;
+    WriteUint32(u: any): void;
+    WriteUint7(i: any): void;
+    WriteITF8(i: any): void;
+    WriteByteNeg(b: any): void;
+}

package/dist/htscodecs/iostream.js

@@ -0,0 +1,243 @@
+"use strict";
+/*
+ * Copyright (c) 2019 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.
+ */
+// Turn a buffer into a fake stream with get / put commands.
+// This enables up to closely match the published pseudocode.
+module.exports = class IOStream {
+    constructor(buf, start_pos = 0, size = 0) {
+        if (size != 0) {
+            this.buf = new Uint8Array(size);
+            this.length = size;
+        }
+        else {
+            this.buf = buf;
+            this.length = buf.length;
+        }
+        this.dataView = new DataView(this.buf.buffer);
+        this.pos = start_pos;
+    }
+    // ----------
+    // Reading
+    EOF() {
+        return this.pos >= this.length;
+    }
+    ReadData(len) {
+        var A = this.buf.slice(this.pos, this.pos + len);
+        this.pos += len;
+        return A;
+    }
+    ReadByte() {
+        const b = this.buf[this.pos];
+        this.pos++;
+        return b;
+    }
+    ReadChar() {
+        const b = this.buf[this.pos];
+        this.pos++;
+        return String.fromCharCode(b);
+    }
+    ReadUint16() {
+        var i = this.ReadByte();
+        i |= this.ReadByte() << 8;
+        return i;
+    }
+    ReadUint32() {
+        const i = this.dataView.getInt32(this.pos, true);
+        this.pos += 4;
+        return i;
+    }
+    // nul terminated string
+    ReadString() {
+        var s = '';
+        do {
+            var b = this.buf[this.pos++];
+            if (b)
+                s += String.fromCharCode(b);
+        } while (b);
+        return s;
+    }
+    //    ReadUint7() {
+    //	// Variable sized unsigned integers
+    //	var i = 0;
+    //	var s = 0;
+    //	do {
+    //	    var c = this.ReadByte();
+    //	    i = i | ((c & 0x7f)<<s);
+    //	    s += 7;
+    //	} while ((c & 0x80))
+    //
+    //	return i;
+    //    }
+    ReadUint7() {
+        // Variable sized unsigned integers
+        var i = 0;
+        do {
+            var c = this.ReadByte();
+            i = (i << 7) | (c & 0x7f);
+        } while (c & 0x80);
+        return i;
+    }
+    ReadITF8() {
+        var i = this.buf[this.pos];
+        this.pos++;
+        //process.stderr.write("i="+i+"\n");
+        if (i >= 0xf0) {
+            // 1111xxxx => +4 bytes
+            i = (i & 0x0f) << 28;
+            i +=
+                (this.buf[this.pos + 0] << 20) +
+                    (this.buf[this.pos + 1] << 12) +
+                    (this.buf[this.pos + 2] << 4) +
+                    (this.buf[this.pos + 3] >> 4);
+            this.pos += 4;
+            //process.stderr.write("  4i="+i+"\n");
+        }
+        else if (i >= 0xe0) {
+            // 1110xxxx => +3 bytes
+            i = (i & 0x0f) << 24;
+            i +=
+                (this.buf[this.pos + 0] << 16) +
+                    (this.buf[this.pos + 1] << 8) +
+                    (this.buf[this.pos + 2] << 0);
+            this.pos += 3;
+            //process.stderr.write("  3i="+i+"\n");
+        }
+        else if (i >= 0xc0) {
+            // 110xxxxx => +2 bytes
+            i = (i & 0x1f) << 16;
+            i += (this.buf[this.pos + 0] << 8) + (this.buf[this.pos + 1] << 0);
+            this.pos += 2;
+            //process.stderr.write("  2i="+i+"\n");
+        }
+        else if (i >= 0x80) {
+            // 10xxxxxx => +1 bytes
+            i = (i & 0x3f) << 8;
+            i += this.buf[this.pos];
+            this.pos++;
+            //process.stderr.write("  1i="+i+"\n");
+        }
+        else {
+            // 0xxxxxxx => +0 bytes
+        }
+        return i;
+    }
+    // ----------
+    // Writing
+    WriteByte(b) {
+        this.buf[this.pos++] = b;
+    }
+    WriteChar(b) {
+        this.buf[this.pos++] = b.charCodeAt(0);
+    }
+    WriteString(str) {
+        for (var i = 0; i < str.length; i++)
+            this.buf[this.pos++] = str.charCodeAt(i);
+        this.buf[this.pos++] = 0;
+    }
+    WriteData(buf, len) {
+        for (var i = 0; i < len; i++)
+            this.buf[this.pos++] = buf[i];
+    }
+    WriteStream(stream) {
+        this.WriteData(stream.buf, stream.pos);
+    }
+    WriteUint16(u) {
+        //this.buf.writeInt16LE(u, this.pos);
+        this.WriteByte(u & 0xff);
+        this.WriteByte((u >> 8) & 0xff);
+    }
+    WriteUint32(u) {
+        this.buf.writeInt32LE(u, this.pos);
+        this.pos += 4;
+    }
+    //    WriteUint7(i) {
+    //	do {
+    //	    this.WriteByte((i & 0x7f) | ((i > 0x80) << 7));
+    //	    i >>= 7;
+    //	} while (i > 0);
+    //    }
+    WriteUint7(i) {
+        var s = 0;
+        var X = i;
+        do {
+            s += 7;
+            X >>= 7;
+        } while (X > 0);
+        do {
+            s -= 7;
+            this.WriteByte(((i >> s) & 0x7f) + ((s > 0) << 7));
+        } while (s > 0);
+    }
+    WriteITF8(i) {
+        // Horrid, ITF8 is unsigned, but we still write signed into it
+        if (i < 0)
+            i = (1 << 32) + i;
+        if (i <= 0x0000007f) {
+            // 1 byte
+            this.buf[this.pos++] = i;
+        }
+        else if (i <= 0x00003fff) {
+            // 2 bytes
+            this.buf[this.pos++] = 0x80 | Math.floor(i / 256);
+            this.buf[this.pos++] = i & 0xff;
+        }
+        else if (i < 0x0001ffff) {
+            // 3 bytes
+            this.buf[this.pos++] = 0xc0 | Math.floor(i / 65536);
+            this.buf[this.pos++] = Math.floor(i / 256) & 0xff;
+            this.buf[this.pos++] = i & 0xff;
+        }
+        else if (i < 0x0fffffff) {
+            // 4 bytes
+            this.buf[this.pos++] = 0xe0 | Math.floor(i / 16777216);
+            this.buf[this.pos++] = Math.floor(i / 65536) & 0xff;
+            this.buf[this.pos++] = Math.floor(i / 256) & 0xff;
+            this.buf[this.pos++] = i & 0xff;
+        }
+        else {
+            // 5 bytes; oddly using 4.5 bytes
+            this.buf[this.pos++] = 0xf0 | Math.floor(i / 268435456);
+            this.buf[this.pos++] = Math.floor(i / 1048576) & 0xff;
+            this.buf[this.pos++] = Math.floor(i / 4096) & 0xff;
+            this.buf[this.pos++] = Math.floor(i / 4) & 0xff;
+            this.buf[this.pos++] = i & 0x0f;
+        }
+    }
+    // ----------
+    // Writing from end of buffer going backwards.
+    // Needed by rANS codec.
+    WriteByteNeg(b) {
+        this.buf[--this.pos] = b;
+    }
+};
+//# sourceMappingURL=iostream.js.map

package/dist/htscodecs/iostream.js.map

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

@@ -0,0 +1 @@
+export function decode(src: any): Uint8Array<any>;

package/dist/htscodecs/rans.js

@@ -0,0 +1,213 @@
+"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 IOStream = require('./iostream');
+//----------------------------------------------------------------------
+// rANS primitives itself
+//
+// RansGet* is decoder side
+function RansGetCumulativeFreq(R) {
+    return R & 0xfff;
+}
+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])
+        s++;
+    return s;
+}
+function RansBuildC2S(C) {
+    var C2S = new Array(0x1000);
+    var s = 0;
+    for (var f = 0; f < 0x1000; f++) {
+        while (f >= C[s + 1])
+            s++;
+        C2S[f] = s;
+    }
+    return C2S;
+}
+function RansAdvanceStep(R, c, f) {
+    return f * (R >> 12) + (R & 0xfff) - c;
+}
+function RansRenorm(src, R) {
+    while (R < 1 << 23)
+        R = (R << 8) + src.ReadByte();
+    return R;
+}
+//----------------------------------------------------------------------
+// Main rANS entry function: decodes a compressed src and
+// returns the uncompressed buffer.
+function decode(src) {
+    var stream = new IOStream(src);
+    var order = stream.ReadByte();
+    var n_in = stream.ReadUint32();
+    var n_out = stream.ReadUint32();
+    if (order == 0) {
+        return RansDecode0(stream, n_out);
+    }
+    else {
+        return RansDecode1(stream, n_out);
+    }
+}
+//----------------------------------------------------------------------
+// Order-0 decoder
+// Decode a single table of order-0 frequences,
+// 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++)
+        F[i] = 0;
+    var sym = src.ReadByte();
+    var last_sym = sym;
+    var rle = 0;
+    // Read F[]
+    do {
+        var f = src.ReadITF8();
+        F[sym] = f;
+        if (rle > 0) {
+            rle--;
+            sym++;
+        }
+        else {
+            sym = src.ReadByte();
+            if (sym == last_sym + 1)
+                rle = src.ReadByte();
+        }
+        last_sym = sym;
+    } while (sym != 0);
+    // Compute C[] from F[]
+    C[0] = 0;
+    for (var i = 0; i <= 255; i++)
+        C[i + 1] = C[i] + F[i];
+}
+function RansDecode0(src, nbytes) {
+    // Decode frequencies
+    var F = new Array(256);
+    var C = new Array(256);
+    ReadFrequencies0(src, F, C);
+    // Fast lookup to avoid slow RansGetSymbolFromFreq
+    var C2S = RansBuildC2S(C);
+    // Initialise rANS state
+    var R = new Array(4);
+    for (var i = 0; i < 4; i++)
+        R[i] = src.ReadUint32();
+    // Main decode loop
+    var output = new Uint8Array(nbytes);
+    for (var i = 0; i < nbytes; i++) {
+        var i4 = i % 4;
+        var f = RansGetCumulativeFreq(R[i4]);
+        var s = C2S[f]; // Equiv to RansGetSymbolFromFreq(C, f);
+        output[i] = s;
+        R[i4] = RansAdvanceStep(R[i4], C[s], F[s]);
+        R[i4] = RansRenorm(src, R[i4]);
+    }
+    return output;
+}
+//----------------------------------------------------------------------
+// Order-1 decoder
+// Decode a table of order-1 frequences,
+// filling out the F and C arrays.
+function ReadFrequencies1(src, F, C) {
+    // Initialise; not in the specification - implicit?
+    for (var i = 0; i < 256; i++) {
+        F[i] = new Array(256);
+        C[i] = new Array(256);
+        for (var j = 0; j < 256; j++)
+            F[i][j] = 0;
+    }
+    var sym = src.ReadByte();
+    var last_sym = sym;
+    var rle = 0;
+    // Read F[]
+    do {
+        ReadFrequencies0(src, F[sym], C[sym]);
+        if (rle > 0) {
+            rle--;
+            sym++;
+        }
+        else {
+            sym = src.ReadByte();
+            if (sym == last_sym + 1)
+                rle = src.ReadByte();
+        }
+        last_sym = sym;
+    } while (sym != 0);
+}
+function RansDecode1(src, nbytes) {
+    // Decode frequencies
+    var F = new Array(256);
+    var C = new Array(256);
+    ReadFrequencies1(src, F, C);
+    // Fast lookup to avoid slow RansGetSymbolFromFreq
+    var C2S = new Array(256);
+    for (var i = 0; i < 256; i++)
+        C2S[i] = RansBuildC2S(C[i]);
+    // Initialise rANS state
+    var R = new Array(4);
+    var L = new Array(4);
+    for (var j = 0; j < 4; j++) {
+        R[j] = src.ReadUint32();
+        L[j] = 0;
+    }
+    // Main decode loop
+    var output = new Uint8Array(nbytes);
+    var nbytes4 = Math.floor(nbytes / 4);
+    for (var i = 0; i < nbytes4; i++) {
+        for (var j = 0; j < 4; j++) {
+            var f = RansGetCumulativeFreq(R[j]);
+            //var s = RansGetSymbolFromFreq(C[L[j]], f);
+            var s = C2S[L[j]][f]; // Precomputed version of above
+            output[i + j * nbytes4] = s;
+            R[j] = RansAdvanceStep(R[j], C[L[j]][s], F[L[j]][s]);
+            R[j] = RansRenorm(src, R[j]);
+            L[j] = s;
+        }
+    }
+    // Now deal with the remainder if buffer size is not a multiple of 4,
+    // using rANS state 3 exclusively.  (It'd have been nice to have
+    // designed this to just act as if we kept going with a bail out.)
+    i = 4 * i;
+    while (i < nbytes) {
+        var f = RansGetCumulativeFreq(R[3]);
+        var s = RansGetSymbolFromFreq(C[L[3]], f);
+        output[i++] = s;
+        R[3] = RansAdvanceStep(R[3], C[L[3]][s], F[L[3]][s]);
+        R[3] = RansRenorm(src, R[3]);
+        L[3] = s;
+    }
+    return output;
+}
+module.exports = { decode };
+//# sourceMappingURL=rans.js.map

package/dist/htscodecs/rans.js.map

@@ -0,0 +1 @@
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package/dist/htscodecs/rans4x16.d.ts

@@ -0,0 +1 @@
+export function decode(src: any): any;