@gmod/cram 6.0.0 → 7.0.0

package/esm/htscodecs/rans4x16.js.map

@@ -1 +0,0 @@
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package/esm/htscodecs/tok3.d.ts

@@ -1 +0,0 @@
-export declare function decode(src: any, len: any, separator: any): string;

package/esm/htscodecs/tok3.js

@@ -1,167 +0,0 @@
-/* eslint-disable no-var */
-// @ts-nocheck
-/*
- * 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.
- */
-// Name tokeniser
-//
-// This is a reference implementation designed to match the
-// written specification as closely as possible.  It is *NOT*
-// an efficient implementation, but see comments below.
-import { concatUint8Array } from "../util.js";
-import arith_gen from "./arith_gen.js";
-import IOStream from "./iostream.js";
-import * as rans from "./rans4x16.js";
-const arith = new arith_gen();
-const TOK_TYPE = 0;
-const TOK_STRING = 1;
-const TOK_CHAR = 2;
-const TOK_DIGITS0 = 3;
-const TOK_DZLEN = 4;
-const TOK_DUP = 5;
-const TOK_DIFF = 6;
-const TOK_DIGITS = 7;
-const TOK_DELTA = 8;
-const TOK_DELTA0 = 9;
-const TOK_MATCH = 10;
-const TOK_NOP = 11;
-const TOK_END = 12;
-// ----------------------------------------------------------------------
-// Token byte streams
-function DecodeTokenByteStreams(src, in_size, use_arith, nnames) {
-    let t = -1;
-    const B = new Array(256);
-    while (!src.EOF()) {
-        const ttype = src.ReadByte();
-        const tok_new = ttype & 128;
-        const tok_dup = ttype & 64;
-        const type = ttype & 63;
-        if (tok_new) {
-            t++;
-            B[t] = new Array(13);
-        }
-        if (type != TOK_TYPE && tok_new) {
-            const M = new Array(nnames - 1).fill(TOK_MATCH);
-            B[t][TOK_TYPE] = new IOStream(concatUint8Array([new Uint8Array(type), M]));
-        }
-        if (tok_dup) {
-            const dup_pos = src.ReadByte();
-            const dup_type = src.ReadByte();
-            B[t][type] = new IOStream(B[dup_pos][dup_type].buf);
-        }
-        else {
-            const clen = src.ReadUint7();
-            const data = src.ReadData(clen);
-            B[t][type] = use_arith ? arith.decode(data) : rans.decode(data);
-            B[t][type] = new IOStream(B[t][type]);
-        }
-    }
-    return B;
-}
-// ----------------------------------------------------------------------
-// Token decode
-function LeftPadNumber(val, len) {
-    let str = val + '';
-    while (str.length < len) {
-        str = '0' + str;
-    }
-    return str;
-}
-function DecodeSingleName(B, N, T, n) {
-    let type = B[0][TOK_TYPE].ReadByte();
-    const dist = B[0][type].ReadUint32();
-    const m = n - dist;
-    if (type == TOK_DUP) {
-        N[n] = N[m];
-        T[n] = T[m];
-        return N[n];
-    }
-    let t = 1;
-    N[n] = '';
-    T[n] = new Array(256);
-    do {
-        type = B[t][TOK_TYPE].ReadByte();
-        switch (type) {
-            case TOK_CHAR:
-                T[n][t] = B[t][TOK_CHAR].ReadChar();
-                break;
-            case TOK_STRING:
-                T[n][t] = B[t][TOK_STRING].ReadString();
-                break;
-            case TOK_DIGITS:
-                T[n][t] = B[t][TOK_DIGITS].ReadUint32();
-                break;
-            case TOK_DIGITS0:
-                var d = B[t][TOK_DIGITS0].ReadUint32();
-                var l = B[t][TOK_DZLEN].ReadByte();
-                T[n][t] = LeftPadNumber(d, l);
-                break;
-            case TOK_DELTA:
-                T[n][t] = (T[m][t] >> 0) + B[t][TOK_DELTA].ReadByte();
-                break;
-            case TOK_DELTA0:
-                var d = (T[m][t] >> 0) + B[t][TOK_DELTA0].ReadByte();
-                var l = T[m][t].length;
-                T[n][t] = LeftPadNumber(d, l);
-                break;
-            case TOK_MATCH:
-                T[n][t] = T[m][t];
-                break;
-            default:
-                T[n][t] = '';
-                break;
-        }
-        N[n] += T[n][t++];
-    } while (type != TOK_END);
-    return N[n];
-}
-// ----------------------------------------------------------------------
-// Main tokeniser decode entry function: decodes a compressed src and
-// returns the uncompressed buffer.
-export function decode(src, len, separator) {
-    var src = new IOStream(src);
-    const ulen = src.ReadUint32();
-    const nnames = src.ReadUint32();
-    const use_arith = src.ReadByte();
-    const B = DecodeTokenByteStreams(src, len, use_arith, nnames);
-    const N = new Array(nnames);
-    const T = new Array(nnames);
-    let str = '';
-    if (separator === undefined) {
-        separator = '\n';
-    }
-    for (let i = 0; i < nnames; i++) {
-        str += DecodeSingleName(B, N, T, i) + separator;
-    }
-    return str;
-}
-//# sourceMappingURL=tok3.js.map

package/esm/htscodecs/tok3.js.map

@@ -1 +0,0 @@
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package/esm/rans/constants.d.ts

@@ -1,4 +0,0 @@
-declare const TF_SHIFT = 12;
-declare const TOTFREQ: number;
-declare const RANS_BYTE_L: number;
-export { RANS_BYTE_L, TF_SHIFT, TOTFREQ };

package/esm/rans/constants.js

@@ -1,5 +0,0 @@
-const TF_SHIFT = 12;
-const TOTFREQ = 1 << TF_SHIFT;
-const RANS_BYTE_L = 1 << 23;
-export { RANS_BYTE_L, TF_SHIFT, TOTFREQ };
-//# sourceMappingURL=constants.js.map

package/esm/rans/constants.js.map

@@ -1 +0,0 @@
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package/esm/rans/d04.d.ts

@@ -1 +0,0 @@
-export default function uncompress(input: any, D: any, syms: any, out: any): void;

package/esm/rans/d04.js

@@ -1,94 +0,0 @@
-// @ts-nocheck
-import { CramMalformedError } from "../errors.js";
-import { TF_SHIFT } from "./constants.js";
-import Decoding from "./decoding.js";
-// Inline constants for performance
-const RANS_BYTE_L = 8388608; // 1 << 23
-const MASK = 4095; // (1 << 12) - 1
-export default function uncompress(
-/* ByteBuffer */ input, 
-/* Decoding.AriDecoder */ D, 
-/* Decoding.Symbol[] */ syms, 
-/* ByteBuffer */ out) {
-    let rans0 = input.getInt();
-    let rans1 = input.getInt();
-    let rans2 = input.getInt();
-    let rans3 = input.getInt();
-    const /* int */ outputSize = out.remaining();
-    const /* int */ outputEnd = outputSize & ~3;
-    const D_R = D.R;
-    for (let i = 0; i < outputEnd; i += 4) {
-        const /* byte */ c0 = D_R[rans0 & MASK];
-        const /* byte */ c1 = D_R[rans1 & MASK];
-        const /* byte */ c2 = D_R[rans2 & MASK];
-        const /* byte */ c3 = D_R[rans3 & MASK];
-        // Inline putAt to avoid function call overhead
-        out._buffer[i] = c0;
-        out._buffer[i + 1] = c1;
-        out._buffer[i + 2] = c2;
-        out._buffer[i + 3] = c3;
-        const sym0 = syms[0xff & c0];
-        const sym1 = syms[0xff & c1];
-        const sym2 = syms[0xff & c2];
-        const sym3 = syms[0xff & c3];
-        rans0 = sym0.freq * (rans0 >> TF_SHIFT) + (rans0 & MASK) - sym0.start;
-        rans1 = sym1.freq * (rans1 >> TF_SHIFT) + (rans1 & MASK) - sym1.start;
-        rans2 = sym2.freq * (rans2 >> TF_SHIFT) + (rans2 & MASK) - sym2.start;
-        rans3 = sym3.freq * (rans3 >> TF_SHIFT) + (rans3 & MASK) - sym3.start;
-        // Inline renormalize to avoid function call overhead
-        if (rans0 < RANS_BYTE_L) {
-            do {
-                rans0 = (rans0 << 8) | (0xff & input.get());
-            } while (rans0 < RANS_BYTE_L);
-        }
-        if (rans1 < RANS_BYTE_L) {
-            do {
-                rans1 = (rans1 << 8) | (0xff & input.get());
-            } while (rans1 < RANS_BYTE_L);
-        }
-        if (rans2 < RANS_BYTE_L) {
-            do {
-                rans2 = (rans2 << 8) | (0xff & input.get());
-            } while (rans2 < RANS_BYTE_L);
-        }
-        if (rans3 < RANS_BYTE_L) {
-            do {
-                rans3 = (rans3 << 8) | (0xff & input.get());
-            } while (rans3 < RANS_BYTE_L);
-        }
-    }
-    out.setPosition(outputEnd);
-    let /* byte */ c;
-    switch (outputSize & 3) {
-        case 0:
-            break;
-        case 1:
-            c = D.R[Decoding.get(rans0, TF_SHIFT)];
-            Decoding.advanceSymbol(rans0, input, syms[0xff & c], TF_SHIFT);
-            out.put(c);
-            break;
-        case 2:
-            c = D.R[Decoding.get(rans0, TF_SHIFT)];
-            Decoding.advanceSymbol(rans0, input, syms[0xff & c], TF_SHIFT);
-            out.put(c);
-            c = D.R[Decoding.get(rans1, TF_SHIFT)];
-            Decoding.advanceSymbol(rans1, input, syms[0xff & c], TF_SHIFT);
-            out.put(c);
-            break;
-        case 3:
-            c = D.R[Decoding.get(rans0, TF_SHIFT)];
-            Decoding.advanceSymbol(rans0, input, syms[0xff & c], TF_SHIFT);
-            out.put(c);
-            c = D.R[Decoding.get(rans1, TF_SHIFT)];
-            Decoding.advanceSymbol(rans1, input, syms[0xff & c], TF_SHIFT);
-            out.put(c);
-            c = D.R[Decoding.get(rans2, TF_SHIFT)];
-            Decoding.advanceSymbol(rans2, input, syms[0xff & c], TF_SHIFT);
-            out.put(c);
-            break;
-        default:
-            throw new CramMalformedError('invalid output size encountered during rANS decoding');
-    }
-    out.setPosition(0);
-}
-//# sourceMappingURL=d04.js.map

package/esm/rans/d04.js.map

@@ -1 +0,0 @@
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package/esm/rans/d14.d.ts

@@ -1 +0,0 @@
-export default function uncompress(input: any, output: any, D: any, syms: any): void;

package/esm/rans/d14.js

@@ -1,93 +0,0 @@
-// @ts-nocheck
-import { TF_SHIFT } from "./constants.js";
-// Inline constants for performance
-const RANS_BYTE_L = 8388608; // 1 << 23
-const MASK = 4095; // (1 << 12) - 1
-export default function uncompress(
-/* ByteBuffer */ input, 
-/* ByteBuffer */ output, 
-/* Decoding.AriDecoder[] */ D, 
-/* Decoding.Symbol[][] */ syms) {
-    const /* int */ outputSize = output.remaining();
-    let rans0 = input.getInt();
-    let rans1 = input.getInt();
-    let rans2 = input.getInt();
-    let rans7 = input.getInt();
-    const /* int */ isz4 = outputSize >> 2;
-    let /* int */ i0 = 0;
-    let /* int */ i1 = isz4;
-    let /* int */ i2 = 2 * isz4;
-    let /* int */ i7 = 3 * isz4;
-    let /* int */ l0 = 0;
-    let /* int */ l1 = 0;
-    let /* int */ l2 = 0;
-    let /* int */ l7 = 0;
-    for (; i0 < isz4; i0 += 1, i1 += 1, i2 += 1, i7 += 1) {
-        const D_l0_R = D[l0].R;
-        const D_l1_R = D[l1].R;
-        const D_l2_R = D[l2].R;
-        const D_l7_R = D[l7].R;
-        const /* int */ c0 = 0xff & D_l0_R[rans0 & MASK];
-        const /* int */ c1 = 0xff & D_l1_R[rans1 & MASK];
-        const /* int */ c2 = 0xff & D_l2_R[rans2 & MASK];
-        const /* int */ c7 = 0xff & D_l7_R[rans7 & MASK];
-        // Inline putAt to avoid function call overhead
-        output._buffer[i0] = c0;
-        output._buffer[i1] = c1;
-        output._buffer[i2] = c2;
-        output._buffer[i7] = c7;
-        const sym_l0_c0 = syms[l0][c0];
-        const sym_l1_c1 = syms[l1][c1];
-        const sym_l2_c2 = syms[l2][c2];
-        const sym_l7_c7 = syms[l7][c7];
-        rans0 =
-            sym_l0_c0.freq * (rans0 >> TF_SHIFT) + (rans0 & MASK) - sym_l0_c0.start;
-        rans1 =
-            sym_l1_c1.freq * (rans1 >> TF_SHIFT) + (rans1 & MASK) - sym_l1_c1.start;
-        rans2 =
-            sym_l2_c2.freq * (rans2 >> TF_SHIFT) + (rans2 & MASK) - sym_l2_c2.start;
-        rans7 =
-            sym_l7_c7.freq * (rans7 >> TF_SHIFT) + (rans7 & MASK) - sym_l7_c7.start;
-        // Inline renormalize to avoid function call overhead
-        if (rans0 < RANS_BYTE_L) {
-            do {
-                rans0 = (rans0 << 8) | (0xff & input.get());
-            } while (rans0 < RANS_BYTE_L);
-        }
-        if (rans1 < RANS_BYTE_L) {
-            do {
-                rans1 = (rans1 << 8) | (0xff & input.get());
-            } while (rans1 < RANS_BYTE_L);
-        }
-        if (rans2 < RANS_BYTE_L) {
-            do {
-                rans2 = (rans2 << 8) | (0xff & input.get());
-            } while (rans2 < RANS_BYTE_L);
-        }
-        if (rans7 < RANS_BYTE_L) {
-            do {
-                rans7 = (rans7 << 8) | (0xff & input.get());
-            } while (rans7 < RANS_BYTE_L);
-        }
-        l0 = c0;
-        l1 = c1;
-        l2 = c2;
-        l7 = c7;
-    }
-    // Remainder
-    for (; i7 < outputSize; i7 += 1) {
-        const /* int */ c7 = 0xff & D[l7].R[rans7 & MASK];
-        // Inline putAt to avoid function call overhead
-        output._buffer[i7] = c7;
-        // Inline advanceSymbol to avoid function call overhead
-        const sym = syms[l7][c7];
-        rans7 = sym.freq * (rans7 >> TF_SHIFT) + (rans7 & MASK) - sym.start;
-        if (rans7 < RANS_BYTE_L) {
-            do {
-                rans7 = (rans7 << 8) | (0xff & input.get());
-            } while (rans7 < RANS_BYTE_L);
-        }
-        l7 = c7;
-    }
-}
-//# sourceMappingURL=d14.js.map

package/esm/rans/d14.js.map

@@ -1 +0,0 @@
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package/esm/rans/decoding.d.ts

@@ -1,27 +0,0 @@
-declare class FC {
-    constructor();
-}
-declare class AriDecoder {
-    constructor();
-}
-declare class DecodingSymbol {
-    constructor();
-}
-declare function symbolInit(sym: any, start: any, freq: any): void;
-declare function advanceStep(r: any, start: any, freq: any, scaleBits: any): number;
-declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
-declare function get(/* final int */ r: any, /* final int */ scaleBits: any): number;
-declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
-declare function renormalize(r: any, pptr: any): any;
-declare const _default: {
-    FC: typeof FC;
-    AriDecoder: typeof AriDecoder;
-    DecodingSymbol: typeof DecodingSymbol;
-    symbolInit: typeof symbolInit;
-    advanceStep: typeof advanceStep;
-    advanceSymbolStep: typeof advanceSymbolStep;
-    get: typeof get;
-    advanceSymbol: typeof advanceSymbol;
-    renormalize: typeof renormalize;
-};
-export default _default;

package/esm/rans/decoding.js

@@ -1,117 +0,0 @@
-// @ts-nocheck
-import { CramMalformedError } from "../errors.js";
-import { RANS_BYTE_L } from "./constants.js";
-class FC {
-    // int F, C;
-    constructor() {
-        this.F = undefined;
-        this.C = undefined;
-    }
-}
-class AriDecoder {
-    // final FC[] fc = new FC[256];
-    // byte[] R;
-    constructor() {
-        // Use two parallel arrays instead of array of objects for better cache efficiency
-        this.fcF = new Array(256);
-        this.fcC = new Array(256);
-        this.R = null;
-    }
-}
-class DecodingSymbol {
-    // int start; // Start of range.
-    // int freq; // Symbol frequency.
-    constructor() {
-        this.start = undefined;
-        this.freq = undefined;
-    }
-}
-// Initialize a decoder symbol to start "start" and frequency "freq"
-function symbolInit(sym, start, freq) {
-    if (!(start <= 1 << 16)) {
-        throw new CramMalformedError('assertion failed: start <= 1<<16');
-    }
-    if (!(freq <= (1 << 16) - start)) {
-        throw new CramMalformedError('assertion failed: freq <= 1<<16');
-    }
-    sym.start = start;
-    sym.freq = freq;
-}
-// Advances in the bit stream by "popping" a single symbol with range start
-// "start" and frequency "freq". All frequencies are assumed to sum to
-// "1 << scaleBits".
-// No renormalization or output happens.
-/* private static int */ function advanceStep(
-/* final int */ r, 
-/* final int */ start, 
-/* final int */ freq, 
-/* final int */ scaleBits) {
-    /* final int */ const mask = (1 << scaleBits) - 1;
-    // s, x = D(x)
-    return freq * (r >> scaleBits) + (r & mask) - start;
-}
-// Equivalent to RansDecAdvanceStep that takes a symbol.
-/* static int  */ function advanceSymbolStep(
-/* final int */ r, 
-/* final RansDecSymbol */ sym, 
-/* final int */ scaleBits) {
-    return advanceStep(r, sym.start, sym.freq, scaleBits);
-}
-// Returns the current cumulative frequency (map it to a symbol yourself!)
-/* static int */ function get(/* final int */ r, /* final int */ scaleBits) {
-    return r & ((1 << scaleBits) - 1);
-}
-// Advances in the bit stream by "popping" a single symbol with range start
-// "start" and frequency "freq". All frequencies are assumed to sum to
-// "1 << scaleBits",
-// and the resulting bytes get written to ptr (which is updated).
-/* private static int */ function advance(
-/* int */ r, 
-/* final ByteBuffer */ pptr, 
-/* final int */ start, 
-/* final int */ freq, 
-/* final int */ scaleBits) {
-    /* final int */ const mask = (1 << scaleBits) - 1;
-    // s, x = D(x)
-    r = freq * (r >> scaleBits) + (r & mask) - start;
-    // re-normalize
-    if (r < RANS_BYTE_L) {
-        do {
-            /* final int */ const b = 0xff & pptr.get();
-            r = (r << 8) | b;
-        } while (r < RANS_BYTE_L);
-    }
-    return r;
-}
-// Equivalent to RansDecAdvance that takes a symbol.
-/*  static int */ function advanceSymbol(
-/* final int */ r, 
-/* final ByteBuffer */ pptr, 
-/* final RansDecSymbol */ sym, 
-/* final int */ scaleBits) {
-    return advance(r, pptr, sym.start, sym.freq, scaleBits);
-}
-// Re-normalize.
-/*  static int */ function renormalize(
-/* int */ r, 
-/* final ByteBuffer */ pptr) {
-    // re-normalize
-    if (r < RANS_BYTE_L) {
-        do {
-            r = (r << 8) | (0xff & pptr.get());
-        } while (r < RANS_BYTE_L);
-    }
-    return r;
-}
-export default {
-    FC,
-    AriDecoder,
-    DecodingSymbol,
-    symbolInit,
-    advanceStep,
-    advanceSymbolStep,
-    get,
-    advanceSymbol,
-    renormalize,
-};
-//# sourceMappingURL=decoding.js.map

package/esm/rans/decoding.js.map

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package/esm/rans/frequencies.d.ts

@@ -1,2 +0,0 @@
-export declare function readStatsO0(cp: any, decoder: any, syms: any): void;
-export declare function readStatsO1(cp: any, D: any, syms: any): void;