@gmod/cram 6.0.0 → 7.0.0

package/dist/htscodecs/arith_sh.js

@@ -1,134 +0,0 @@
-"use strict";
-// @ts-nocheck
-Object.defineProperty(exports, "__esModule", { value: true });
-/*
- * 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
-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 (let 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) {
-        const 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 (let i = 0; i < 5; i++) {
-            this.RangeShiftLow(dst);
-        }
-    }
-}
-exports.default = RangeCoder;
-//# sourceMappingURL=arith_sh.js.map

package/dist/htscodecs/arith_sh.js.map

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

@@ -1,6 +0,0 @@
-export default class ByteModel {
-    constructor(max_sym?: number);
-    ModelDecode(src: any, rc: any): any;
-    ModelRenormalise(): void;
-    ModelEncode(dst: any, rc: any, sym: any): void;
-}

package/dist/htscodecs/byte_model.js

@@ -1,121 +0,0 @@
-"use strict";
-/* eslint-disable no-var */
-// @ts-nocheck
-Object.defineProperty(exports, "__esModule", { value: true });
-/*
- * 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;
-class ByteModel {
-    constructor(max_sym = 256) {
-        this.total_freq = max_sym;
-        this.max_sym = max_sym - 1;
-        this.S = [];
-        this.F = [];
-        for (let i = 0; i <= this.max_sym; i++) {
-            this.S[i] = i;
-            this.F[i] = 1;
-        }
-    }
-    ModelDecode(src, rc) {
-        // Find symbol
-        const freq = rc.RangeGetFrequency(this.total_freq);
-        // Linear scan to find cumulative frequency 'freq'
-        let acc = 0;
-        let 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
-        const sym = this.S[x];
-        if (x > 0 && this.F[x] > this.F[x - 1]) {
-            let 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 (let 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
-        let 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]) {
-            let 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;
-        }
-    }
-}
-exports.default = ByteModel;
-//# sourceMappingURL=byte_model.js.map

package/dist/htscodecs/byte_model.js.map

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package/dist/htscodecs/fqzcomp.d.ts

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

package/dist/htscodecs/fqzcomp.js

@@ -1,346 +0,0 @@
-"use strict";
-/* eslint-disable no-var */
-// @ts-nocheck
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.decode = decode;
-/*
- * 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.
- */
-const arith_sh_ts_1 = __importDefault(require("./arith_sh.js"));
-const byte_model_ts_1 = __importDefault(require("./byte_model.js"));
-const iostream_ts_1 = __importDefault(require("./iostream.js"));
-// ----------------------------------------------------------------------
-// Main arithmetic entry function: decodes a compressed src and
-// returns the uncompressed buffer.
-function read_array(src, tab, size) {
-    let j = 0; // array value
-    let z = 0; // array index: tab[j]
-    let last = -1;
-    // Remove first level of run-length encoding
-    const R = new Array(1024); // runs
-    while (z < size) {
-        const run = src.ReadByte();
-        R[j++] = run;
-        z += run;
-        if (run == last) {
-            let copy = src.ReadByte();
-            z += run * copy;
-            while (copy--) {
-                R[j++] = run;
-            }
-        }
-        last = run;
-    }
-    // Now expand runs in R to tab, noting 255 is max run
-    let i = 0;
-    j = 0;
-    z = 0;
-    while (z < size) {
-        let run_len = 0;
-        do {
-            var part = R[j++];
-            run_len += part;
-        } while (part == 255);
-        while (run_len--) {
-            tab[z++] = i;
-        }
-        i++;
-    }
-}
-const QMAX = 256;
-const FLAG_DEDUP = 2;
-const FLAG_FLEN = 4;
-const FLAG_SEL = 8; // whether selector is used in context
-const FLAG_QMAP = 16;
-const FLAG_PTAB = 32;
-const FLAG_DTAB = 64;
-const FLAG_QTAB = 128;
-const GFLAG_MULTI_PARAM = 1;
-const GFLAG_HAVE_STAB = 2;
-const GFLAG_DO_REV = 4;
-// Compute a new context from our current state and qual q
-function fqz_update_ctx(params, state, q) {
-    let last = params.context;
-    state.qctx = (state.qctx << params.qshift) + params.qtab[q]; // >>> 0
-    last += (state.qctx & ((1 << params.qbits) - 1)) << params.qloc; // >>> 0
-    if (params.do_pos) {
-        last += params.ptab[Math.min(state.p, 1023)] << params.ploc;
-    }
-    if (params.do_delta) {
-        last += params.dtab[Math.min(state.delta, 255)] << params.dloc;
-        // Is it better to use q here or qtab[q]?
-        // If qtab[q] we can map eg [a-z0-9A-Z]->0 ,->1 and have
-        // delta being a token number count into comma separated lists?
-        state.delta += state.prevq != q ? 1 : 0;
-        state.prevq = q;
-    }
-    if (params.do_sel) {
-        last += state.s << params.sloc;
-    }
-    state.p--;
-    return last & 0xffff;
-}
-function decode_fqz_single_param(src) {
-    const p = {}; // params
-    // Load FQZ parameters
-    p.context = src.ReadUint16();
-    p.pflags = src.ReadByte();
-    p.do_dedup = p.pflags & FLAG_DEDUP;
-    p.fixed_len = p.pflags & FLAG_FLEN;
-    p.do_sel = p.pflags & FLAG_SEL;
-    p.do_qmap = p.pflags & FLAG_QMAP;
-    p.do_pos = p.pflags & FLAG_PTAB;
-    p.do_delta = p.pflags & FLAG_DTAB;
-    p.do_qtab = p.pflags & FLAG_QTAB;
-    p.max_sym = src.ReadByte();
-    let x = src.ReadByte();
-    p.qbits = x >> 4;
-    p.qshift = x & 15;
-    x = src.ReadByte();
-    p.qloc = x >> 4;
-    p.sloc = x & 15;
-    x = src.ReadByte();
-    p.ploc = x >> 4;
-    p.dloc = x & 15;
-    // Qual map, eg to "unbin" Illumina qualities
-    p.qmap = new Array(256);
-    if (p.pflags & FLAG_QMAP) {
-        for (var i = 0; i < p.max_sym; i++) {
-            p.qmap[i] = src.ReadByte();
-        }
-    }
-    else {
-        // Useful optimisation to speed up main loop
-        for (var i = 0; i < 256; i++) {
-            p.qmap[i] = i;
-        } // NOP
-    }
-    // Read tables
-    p.qtab = new Array(1024);
-    if (p.qbits > 0 && p.pflags & FLAG_QTAB) {
-        read_array(src, p.qtab, 256);
-    }
-    else {
-        // Useful optimisation to speed up main loop
-        for (var i = 0; i < 256; i++) {
-            p.qtab[i] = i;
-        } // NOP
-    }
-    p.ptab = new Array(1024);
-    if (p.pflags & FLAG_PTAB) {
-        read_array(src, p.ptab, 1024);
-    }
-    p.dtab = new Array(256);
-    if (p.pflags & FLAG_DTAB) {
-        read_array(src, p.dtab, 256);
-    }
-    return p;
-}
-function decode_fqz_params(src) {
-    const gparams = {
-        max_sym: 0,
-    };
-    // Check fqz format version
-    const vers = src.ReadByte();
-    if (vers != 5) {
-        console.error('Invalid FQZComp version number');
-        return;
-    }
-    const gflags = src.ReadByte();
-    const nparam = gflags & GFLAG_MULTI_PARAM ? src.ReadByte() : 1;
-    let max_sel = gflags.nparam > 1 ? gflags.nparam - 1 : 0; // Note max_sel, not num_sel
-    const stab = new Array(256);
-    if (gflags & GFLAG_HAVE_STAB) {
-        max_sel = src.ReadByte();
-        read_array(src, stab, 256);
-    }
-    else {
-        for (var i = 0; i < nparam; i++) {
-            stab[i] = i;
-        }
-        for (; i < 256; i++) {
-            stab[i] = nparam - 1;
-        }
-    }
-    gparams.do_rev = gflags & GFLAG_DO_REV;
-    gparams.stab = stab;
-    gparams.max_sel = max_sel;
-    gparams.params = new Array(gparams.nparam);
-    for (let p = 0; p < nparam; p++) {
-        gparams.params[p] = decode_fqz_single_param(src);
-        if (gparams.max_sym < gparams.params[p].max_sym) {
-            gparams.max_sym = gparams.params[p].max_sym;
-        }
-    }
-    return gparams;
-}
-function fqz_create_models(gparams) {
-    const model = {};
-    model.qual = new Array(1 << 16);
-    for (var i = 0; i < 1 << 16; i++) {
-        model.qual[i] = new byte_model_ts_1.default(gparams.max_sym + 1);
-    } // +1 as max value not num. values
-    model.len = new Array(4);
-    for (var i = 0; i < 4; i++) {
-        model.len[i] = new byte_model_ts_1.default(256);
-    }
-    model.rev = new byte_model_ts_1.default(2);
-    model.dup = new byte_model_ts_1.default(2);
-    if (gparams.max_sel > 0) {
-        model.sel = new byte_model_ts_1.default(gparams.max_sel + 1);
-    } // +1 as max value not num. values
-    return model;
-}
-// Initialise a new record, updating state.
-// Returns 1 if dup, otherwise 0
-function decode_fqz_new_record(src, rc, gparams, model, state, rev) {
-    // Parameter selector
-    state.s = gparams.max_sel > 0 ? model.sel.ModelDecode(src, rc) : 0;
-    state.x = gparams.stab[state.s];
-    const params = gparams.params[state.x];
-    // Reset contexts at the start of each new record
-    if (params.fixed_len >= 0) {
-        // Not fixed or fixed but first record
-        var len = model.len[0].ModelDecode(src, rc);
-        len |= model.len[1].ModelDecode(src, rc) << 8;
-        len |= model.len[2].ModelDecode(src, rc) << 16;
-        len |= model.len[3].ModelDecode(src, rc) << 24;
-        if (params.fixed_len > 0) {
-            params.fixed_len = -len;
-        }
-    }
-    else {
-        len = -params.fixed_len;
-    }
-    state.len = len;
-    if (gparams.do_rev) {
-        rev[state.rec] = model.rev.ModelDecode(src, rc);
-    }
-    state.is_dup = 0;
-    if (params.pflags & FLAG_DEDUP) {
-        if (model.dup.ModelDecode(src, rc)) {
-            state.is_dup = 1;
-        }
-    }
-    state.p = len; // number of remaining bytes in this record
-    state.delta = 0;
-    state.qctx = 0;
-    state.prevq = 0;
-    state.rec++;
-}
-function decode_fqz(src, q_lens) {
-    // Decode parameter block
-    const n_out = src.ReadUint7();
-    const gparams = decode_fqz_params(src);
-    if (!gparams) {
-        return;
-    }
-    var params = gparams.params;
-    const rev = new Array(q_lens.length);
-    // Create initial models
-    const model = fqz_create_models(gparams);
-    // Create our entropy encoder and output buffers
-    const rc = new arith_sh_ts_1.default(src);
-    rc.RangeStartDecode(src);
-    const output = new Uint8Array(n_out);
-    // Internal FQZ state
-    const state = {
-        qctx: 0, // Qual-only sub-context
-        prevq: 0, // Previous quality value
-        delta: 0, // Running delta (q vs prevq)
-        p: 0, // Number of bases left in current record
-        s: 0, // Current parameter selector value (0 if unused)
-        x: 0, // "stab" tabulated copy of s
-        len: 0, // Length of current string
-        is_dup: 0, // This string is a duplicate of last
-        rec: 0, // Record number
-    };
-    // The main decode loop itself
-    let i = 0; // position in output buffer
-    while (i < n_out) {
-        if (state.p == 0) {
-            decode_fqz_new_record(src, rc, gparams, model, state, rev);
-            if (state.is_dup > 0) {
-                if (model.dup.ModelDecode(src, rc)) {
-                    // Duplicate of last line
-                    for (let x = 0; x < len; x++) {
-                        output[i + x] = output[i + x - state.len];
-                    }
-                    i += state.len;
-                    state.p = 0;
-                    continue;
-                }
-            }
-            q_lens.push(state.len);
-            var params = gparams.params[state.x];
-            var last = params.context;
-        }
-        // Decode the current quality (possibly mapped via qmap)
-        const Q = model.qual[last].ModelDecode(src, rc);
-        // if (params.do_qmap)
-        //    output[i++] = params.qmap[Q];
-        // else
-        //    output[i++] = Q
-        output[i++] = params.qmap[Q]; // optimised version of above
-        last = fqz_update_ctx(params, state, Q);
-    }
-    if (gparams.do_rev) {
-        reverse_qualities(output, n_out, rev, q_lens);
-    }
-    return output;
-}
-function reverse_qualities(qual, qual_len, rev, len) {
-    let rec = 0;
-    let i = 0;
-    while (i < qual_len) {
-        if (rev[rec]) {
-            let j = 0;
-            let k = len[rec] - 1;
-            while (j < k) {
-                const tmp = qual[i + j];
-                qual[i + j] = qual[i + k];
-                qual[i + k] = tmp;
-                j++;
-                k--;
-            }
-        }
-        i += len[rec++];
-    }
-}
-function decode(src, q_lens) {
-    const stream = new iostream_ts_1.default(src);
-    return decode_fqz(stream, q_lens);
-}
-//# sourceMappingURL=fqzcomp.js.map

package/dist/htscodecs/fqzcomp.js.map

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

@@ -1,16 +0,0 @@
-export default class IOStream {
-    buf: Uint8Array;
-    length: number;
-    pos: number;
-    dataView: DataView;
-    constructor(buf: Uint8Array, start_pos?: number, size?: number);
-    EOF(): boolean;
-    ReadData(len: number): Uint8Array<ArrayBuffer>;
-    ReadByte(): number;
-    ReadChar(): string;
-    ReadUint16(): number;
-    ReadUint32(): number;
-    ReadString(): string;
-    ReadUint7(): number;
-    ReadITF8(): number;
-}