@gmod/cram 3.0.6 → 4.0.0

package/esm/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/esm/htscodecs/arith_gen.js.map

@@ -0,0 +1 @@
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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;
+}

package/esm/htscodecs/arith_sh.js

@@ -0,0 +1,128 @@
+"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.
+ */
+// An arithmetic coder, based on Eugene Shelwien's reimplementation of
+// Michael Schindler range coder.
+//
+// Order-0 byte stream of ~/scratch/data/q40b
+// 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 {
+    constructor(src) {
+        this.low = 0;
+        this.range = 0xffffffff;
+        this.code = 0;
+        this.FFnum = 0;
+        this.carry = 0;
+        this.cache = 0;
+    }
+    RangeStartDecode(src) {
+        for (var 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 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)));
+    }
+    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.code -= sym_low * this.range;
+        this.range *= sym_freq;
+        while (this.range < 1 << 24) {
+            this.range *= 256;
+            this.code = this.code * 256 + src.ReadByte();
+        }
+    }
+    RangeShiftLow(dst) {
+        // We know range is < (1<<24) as we got here.  We already have a
+        // cached copy of 8 bits from low.  Is this correct, or does it need
+        // fixing?  Possible scenarios.
+        // 1. Low < 0xff000000 thus low+range < 0xffffffff and cache
+        //    cannot possibly change.  Output cache and as many ffs as needed.
+        // 2. We already detected an overflow in RangeEncode, setting carry.
+        //    In this case output cached byte + 1 and any 00s needed.
+        // 3. Neither case - range is low but we haven't yet detected if we're
+        //    XXffffff or XY000000 scenario.  Increase counter for ff/00s.
+        if ((this.low < 0xff000000) | this.carry) {
+            // cached byte if no overflow, byte+1 otherwise
+            dst.WriteByte(this.cache + this.carry);
+            // Flush any tracked FFs (no carry) or 00s (carry).
+            while (this.FFnum) {
+                dst.WriteByte(this.carry - 1);
+                this.FFnum--;
+            }
+            // Take a copy of top byte ready for next flush
+            this.cache = this.low >>> 24;
+            this.carry = 0;
+        }
+        else {
+            this.FFnum++; // keep track of number of trailing ff/00 bytes to write
+        }
+        this.low <<= 8;
+        this.low >>>= 0; // force to be +ve int
+    }
+    RangeEncode(dst, sym_low, sym_freq, tot_freq) {
+        var 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
+        this.range *= sym_freq;
+        // "low + sym*range < old_low" means we overflow; set carry.
+        // 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)
+                console.log('ERROR: Multiple carry');
+            this.carry = 1;
+        }
+        // Renormalise if range gets too small
+        while (this.range < 1 << 24) {
+            this.range *= 256;
+            this.RangeShiftLow(dst);
+        }
+    }
+    RangeFinishEncode(dst) {
+        for (var i = 0; i < 5; i++)
+            this.RangeShiftLow(dst);
+    }
+};
+//# sourceMappingURL=arith_sh.js.map

package/esm/htscodecs/arith_sh.js.map

@@ -0,0 +1 @@
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package/esm/htscodecs/byte_model.d.ts

@@ -0,0 +1,11 @@
+export = ByteModel;
+declare 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;
+}

package/esm/htscodecs/byte_model.js

@@ -0,0 +1,113 @@
+"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.
+ */
+// An adaptive probability model for encoding and decoding of symbols
+// within a given alphabet, using the range coder to get/put the
+// compressed data.
+const MAX_FREQ = (1 << 16) - 17;
+const STEP = 16;
+module.exports = class ByteModel {
+    constructor(max_sym = 256) {
+        this.total_freq = max_sym;
+        this.max_sym = max_sym - 1;
+        this.S = new Array();
+        this.F = new Array();
+        for (var i = 0; i <= this.max_sym; i++) {
+            this.S[i] = i;
+            this.F[i] = 1;
+        }
+    }
+    ModelDecode(src, rc) {
+        // Find symbol
+        var freq = rc.RangeGetFrequency(this.total_freq);
+        // Linear scan to find cumulative frequency 'freq'
+        var acc = 0;
+        var x = 0;
+        while (acc + this.F[x] <= freq)
+            acc += this.F[x++];
+        //	for (var acc = 0; (acc += this.F[x]) <= freq; x++)
+        //	    ;
+        //	acc -= this.F[x];
+        // Update range coder
+        rc.RangeDecode(src, acc, this.F[x], this.total_freq);
+        // Update model
+        this.F[x] += STEP;
+        this.total_freq += STEP;
+        if (this.total_freq > MAX_FREQ)
+            this.ModelRenormalise();
+        // Keep symbols approximately frequency sorted
+        var sym = this.S[x];
+        if (x > 0 && this.F[x] > this.F[x - 1]) {
+            var tmp = this.F[x];
+            this.F[x] = this.F[x - 1];
+            this.F[x - 1] = tmp;
+            tmp = this.S[x];
+            this.S[x] = this.S[x - 1];
+            this.S[x - 1] = tmp;
+        }
+        return sym;
+    }
+    ModelRenormalise() {
+        // Halve all the frequencies, being careful not to hit zero
+        this.total_freq = 0;
+        for (var i = 0; i <= this.max_sym; i++) {
+            this.F[i] -= Math.floor(this.F[i] / 2);
+            this.total_freq += this.F[i];
+        }
+    }
+    ModelEncode(dst, rc, sym) {
+        // Find cumulative frequency
+        var acc = 0;
+        for (var x = 0; this.S[x] != sym; x++)
+            acc += this.F[x];
+        // Encode
+        rc.RangeEncode(dst, acc, this.F[x], this.total_freq);
+        // Update model
+        this.F[x] += STEP;
+        this.total_freq += STEP;
+        if (this.total_freq > MAX_FREQ)
+            // FIXME x2
+            this.ModelRenormalise();
+        // Keep symbols approximately frequency sorted
+        var sym = this.S[x];
+        if (x > 0 && this.F[x] > this.F[x - 1]) {
+            var tmp = this.F[x];
+            this.F[x] = this.F[x - 1];
+            this.F[x - 1] = tmp;
+            tmp = this.S[x];
+            this.S[x] = this.S[x - 1];
+            this.S[x - 1] = tmp;
+        }
+    }
+};
+//# sourceMappingURL=byte_model.js.map

package/esm/htscodecs/byte_model.js.map

@@ -0,0 +1 @@
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package/esm/htscodecs/fqzcomp.d.ts

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