@gmod/cram 4.0.3 → 4.0.5

package/dist/htscodecs/tok3.js

@@ -1,4 +1,44 @@
 "use strict";
+/* eslint-disable no-var */
+// @ts-nocheck
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+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
@@ -36,26 +76,11 @@
 // 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.
-const IOStream = require('./iostream');
-const rans = require('./rans4x16');
-const arith_gen = require('./arith_gen');
-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;
-}
-var arith = new arith_gen();
+const util_1 = require("../util");
+const arith_gen_1 = __importDefault(require("./arith_gen"));
+const iostream_1 = __importDefault(require("./iostream"));
+const rans = __importStar(require("./rans4x16"));
+const arith = new arith_gen_1.default();
 const TOK_TYPE = 0;
 const TOK_STRING = 1;
 const TOK_CHAR = 2;
@@ -69,59 +94,57 @@ 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) {
-    var t = -1;
-    var B = new Array(256);
+    let t = -1;
+    const B = new Array(256);
     while (!src.EOF()) {
-        var ttype = src.ReadByte();
-        var tok_new = ttype & 128;
-        var tok_dup = ttype & 64;
-        var type = ttype & 63;
+        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) {
-            var M = new Array(nnames - 1).fill(TOK_MATCH);
-            B[t][TOK_TYPE] = new IOStream(concatUint8Array([new Uint8Array(type), M]));
+            const M = new Array(nnames - 1).fill(TOK_MATCH);
+            B[t][TOK_TYPE] = new iostream_1.default((0, util_1.concatUint8Array)([new Uint8Array(type), M]));
         }
         if (tok_dup) {
-            var dup_pos = src.ReadByte();
-            var dup_type = src.ReadByte();
-            B[t][type] = new IOStream(B[dup_pos][dup_type].buf);
+            const dup_pos = src.ReadByte();
+            const dup_type = src.ReadByte();
+            B[t][type] = new iostream_1.default(B[dup_pos][dup_type].buf);
         }
         else {
-            var clen = src.ReadUint7();
-            var data = src.ReadData(clen);
-            if (use_arith)
-                B[t][type] = arith.decode(data);
-            else
-                B[t][type] = rans.decode(data);
-            B[t][type] = new IOStream(B[t][type]);
+            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_1.default(B[t][type]);
         }
     }
     return B;
 }
-//----------------------------------------------------------------------
+// ----------------------------------------------------------------------
 // Token decode
 function LeftPadNumber(val, len) {
-    var str = val + '';
-    while (str.length < len)
+    let str = val + '';
+    while (str.length < len) {
         str = '0' + str;
+    }
     return str;
 }
 function DecodeSingleName(B, N, T, n) {
-    var type = B[0][TOK_TYPE].ReadByte();
-    var dist = B[0][type].ReadUint32();
-    var m = n - dist;
+    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];
     }
-    var t = 1;
+    let t = 1;
     N[n] = '';
     T[n] = new Array(256);
     do {
@@ -160,204 +183,24 @@ function DecodeSingleName(B, N, T, n) {
     } while (type != TOK_END);
     return N[n];
 }
-//----------------------------------------------------------------------
+// ----------------------------------------------------------------------
 // Main tokeniser decode entry function: decodes a compressed src and
 // returns the uncompressed buffer.
 function decode(src, len, separator) {
-    var src = new IOStream(src);
-    var ulen = src.ReadUint32();
-    var nnames = src.ReadUint32();
-    var use_arith = src.ReadByte();
-    var B = DecodeTokenByteStreams(src, len, use_arith, nnames);
-    var N = new Array(nnames);
-    var T = new Array(nnames);
-    var str = '';
-    if (typeof separator === 'undefined')
+    var src = new iostream_1.default(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 (var i = 0; i < nnames; i++)
-        str += DecodeSingleName(B, N, T, i) + separator;
-    return str;
-}
-//----------------------------------------------------------------------
-// Main tokeniser encode function
-// Encoder is trickier than decode as we have a lot of decisions to make.
-// However here we just make a simple guess without anything complex,
-// to demonstrate the basic idea.  See the C implementation for further
-// expansion on this.
-function encode(src, use_arith) {
-    // Convert buffer to array of names
-    var str = src.toString();
-    if (str[str.length - 1] == '\n')
-        str = str.substring(0, str.length - 1);
-    var names = str.split('\n');
-    var out = new IOStream('', 0, str.length * 2 + 10000); // guess max size
-    out.WriteUint32(str.length);
-    out.WriteUint32(names.length);
-    out.WriteByte(use_arith);
-    // Tokenise names
-    var T = new Array(names.length);
-    var H = {};
-    var F = new Array(256).fill(0); // DELTA vs DIGIT frequency
-    var max_tok = 0;
-    var max_len = 0;
-    for (var i = 0; i < names.length; i++) {
-        var [ntok, len] = TokeniseName(T, H, F, names[i], i);
-        if (max_tok < ntok)
-            max_tok = ntok;
-        if (max_len < len)
-            max_len = len;
-    }
-    // Convert tokens to byte streams and serialise
-    for (var tnum = 0; tnum < max_tok; tnum++) {
-        var B = new Array(TOK_END + 1);
-        for (var type = 0; type <= TOK_END; type++)
-            B[type] = new IOStream('', 0, names.length * max_len);
-        FillByteStreams(B, T, tnum, names, max_tok, max_len);
-        SerialiseByteStreams(B, tnum, use_arith, out);
-    }
-    return out.buf.slice(0, out.pos);
-}
-function FillByteStreams(B, T, tnum, names, max_tok, max_len) {
-    // Create byte streams B[]
-    for (var n = 0; n < names.length; n++) {
-        if (tnum > 0 && T[n][0].type == TOK_DUP)
-            continue;
-        if (!T[n][tnum])
-            continue;
-        B[TOK_TYPE].WriteByte(T[n][tnum].type);
-        switch (T[n][tnum].type) {
-            case TOK_DIFF:
-                B[TOK_DIFF].WriteUint32(T[n][tnum].val);
-                break;
-            case TOK_DUP:
-                B[TOK_DUP].WriteUint32(T[n][tnum].val);
-                break;
-            case TOK_STRING:
-                B[TOK_STRING].WriteString(T[n][tnum].val);
-                break;
-            case TOK_CHAR:
-                B[TOK_CHAR].WriteChar(T[n][tnum].val);
-                break;
-            case TOK_DIGITS:
-                B[TOK_DIGITS].WriteUint32(T[n][tnum].val);
-                break;
-            case TOK_DIGITS0:
-                B[TOK_DIGITS0].WriteUint32(T[n][tnum].val);
-                B[TOK_DZLEN].WriteByte(T[n][tnum].val.length);
-                break;
-            case TOK_DELTA:
-                B[T[n][tnum].type].WriteByte(T[n][tnum].val);
-                break;
-            case TOK_DELTA0:
-                B[T[n][tnum].type].WriteByte(T[n][tnum].val);
-                break;
-        }
-    }
-}
-function SerialiseByteStreams(B, tnum, use_arith, out) {
-    // Compress and serialise byte streams B[]
-    for (var type = 0; type <= TOK_END; type++) {
-        if (B[type].pos <= 0)
-            continue;
-        out.WriteByte(type + (type == 0 ? 128 : 0));
-        // IOStream to sized buffer
-        B[type] = B[type].buf.slice(0, B[type].pos);
-        var comp = try_compress(B[type], use_arith);
-        out.WriteUint7(comp.length);
-        out.WriteData(comp, comp.length);
-    }
-}
-function try_compress(src, use_arith) {
-    var best = 1 << 30;
-    var comp;
-    var methods = [0, 1, 64, 65, 128, 129, 193 + 8];
-    for (var i in methods) {
-        var lvl = methods[i];
-        if (lvl & 1 && src.length < 100)
-            continue;
-        if (lvl & 8 && src.length % 4 != 0)
-            continue;
-        try {
-            var tmp = use_arith ? arith.encode(src, lvl) : rans.encode(src, lvl);
-        }
-        catch (e) {
-            var tmp = 0;
-        }
-        if (tmp && best > tmp.length) {
-            best = tmp.length;
-            comp = tmp;
-        }
-    }
-    return comp;
-}
-function TokeniseName(T, H, F, name, n) {
-    var max_len = 0;
-    // Always compare against last name only
-    var p = n - 1;
-    T[n] = new Array(256);
-    if (H[name]) {
-        //console.error(name,H[name],n)
-        T[n][0] = {
-            type: TOK_DUP,
-            val: n - H[name],
-        };
-    }
-    else {
-        T[n][0] = {
-            type: TOK_DIFF,
-            val: n == 0 ? 0 : 1,
-        };
     }
-    H[name] = n;
-    // Splits on alphanumerics, punctuation
-    var tok = name.match(/([a-zA-Z0-9]{1,9})|([^a-zA-Z0-9]+)/g);
-    for (var i = 0; i < tok.length; i++) {
-        var t = i + 1; // token 0 = DIFF vs DUP
-        var type = TOK_STRING;
-        var val = tok[i];
-        if (tok[i].match(/^0+[0-9]*$/g))
-            type = TOK_DIGITS0;
-        else if (tok[i].match(/^[0-9]+$/g))
-            type = TOK_DIGITS;
-        else if (tok[i].length == 1)
-            type = TOK_CHAR;
-        if (p >= 0 && T[p][t]) {
-            if (T[p][t].str == tok[i]) {
-                type = TOK_MATCH;
-                val = '';
-            }
-            else if (T[p][t].type == TOK_DIGITS || T[p][t].type == TOK_DELTA) {
-                var d = val - T[p][t].str;
-                F[t]++;
-                if (d >= 0 && d < 256 && F[t] > n / 2) {
-                    type = TOK_DELTA;
-                    val = d;
-                }
-            }
-            else if ((T[p][t].type == TOK_DIGITS0 || T[p][t].type == TOK_DELTA0) &&
-                T[p][t].str.length == val.length) {
-                var d = val - T[p][t].str;
-                F[t]++;
-                if (d >= 0 && d < 256 && F[t] > n / 2) {
-                    type = TOK_DELTA0;
-                    val = d;
-                }
-            }
-        }
-        T[n][t] = {
-            str: tok[i],
-            val: val,
-            type: type,
-        };
-        if (max_len < T[n][t].val.length + 3)
-            // +3 for integers; 5 -> (Uint32)5
-            max_len = T[n][t].val.length + 3;
-        //console.error(t,T[n][t])
+    for (let i = 0; i < nnames; i++) {
+        str += DecodeSingleName(B, N, T, i) + separator;
     }
-    T[n][++t] = {
-        type: TOK_END,
-    };
-    return [t + 1, max_len];
+    return str;
 }
-module.exports = { encode, decode };
 //# sourceMappingURL=tok3.js.map

package/dist/htscodecs/tok3.js.map

@@ -1 +1 @@
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+{"version":3,"file":"tok3.js","sourceRoot":"","sources":["../../src/htscodecs/tok3.ts"],"names":[],"mappings":";AAAA,2BAA2B;AAC3B,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAgLd,wBAmBC;AAjMD;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,iBAAiB;AACjB,EAAE;AACF,2DAA2D;AAC3D,6DAA6D;AAC7D,uDAAuD;AAEvD,kCAA0C;AAC1C,4DAAmC;AACnC,0DAAiC;AACjC,iDAAkC;AAElC,MAAM,KAAK,GAAG,IAAI,mBAAS,EAAE,CAAA;AAE7B,MAAM,QAAQ,GAAG,CAAC,CAAA;AAClB,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,QAAQ,GAAG,CAAC,CAAA;AAClB,MAAM,WAAW,GAAG,CAAC,CAAA;AACrB,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,OAAO,GAAG,CAAC,CAAA;AACjB,MAAM,QAAQ,GAAG,CAAC,CAAA;AAClB,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,SAAS,GAAG,EAAE,CAAA;AACpB,MAAM,OAAO,GAAG,EAAE,CAAA;AAClB,MAAM,OAAO,GAAG,EAAE,CAAA;AAElB,yEAAyE;AACzE,qBAAqB;AACrB,SAAS,sBAAsB,CAAC,GAAG,EAAE,OAAO,EAAE,SAAS,EAAE,MAAM;IAC7D,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;IAEV,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAExB,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,EAAE,CAAC;QAClB,MAAM,KAAK,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;QAC5B,MAAM,OAAO,GAAG,KAAK,GAAG,GAAG,CAAA;QAC3B,MAAM,OAAO,GAAG,KAAK,GAAG,EAAE,CAAA;QAC1B,MAAM,IAAI,GAAG,KAAK,GAAG,EAAE,CAAA;QAEvB,IAAI,OAAO,EAAE,CAAC;YACZ,CAAC,EAAE,CAAA;YACH,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,EAAE,CAAC,CAAA;QACtB,CAAC;QAED,IAAI,IAAI,IAAI,QAAQ,IAAI,OAAO,EAAE,CAAC;YAChC,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;YAC/C,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,IAAI,kBAAQ,CAAC,IAAA,uBAAgB,EAAC,CAAC,IAAI,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;QAC5E,CAAC;QAED,IAAI,OAAO,EAAE,CAAC;YACZ,MAAM,OAAO,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;YAC9B,MAAM,QAAQ,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;YAC/B,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,kBAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAA;QACrD,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,GAAG,GAAG,CAAC,SAAS,EAAE,CAAA;YAC5B,MAAM,IAAI,GAAG,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAE/B,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YAC/D,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,kBAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;QACvC,CAAC;IACH,CAAC;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,yEAAyE;AACzE,eAAe;AACf,SAAS,aAAa,CAAC,GAAG,EAAE,GAAG;IAC7B,IAAI,GAAG,GAAG,GAAG,GAAG,EAAE,CAAA;IAClB,OAAO,GAAG,CAAC,MAAM,GAAG,GAAG,EAAE,CAAC;QACxB,GAAG,GAAG,GAAG,GAAG,GAAG,CAAA;IACjB,CAAC;IAED,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAS,gBAAgB,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC;IAClC,IAAI,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,CAAA;IACpC,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,UAAU,EAAE,CAAA;IACpC,MAAM,CAAC,GAAG,CAAC,GAAG,IAAI,CAAA;IAElB,IAAI,IAAI,IAAI,OAAO,EAAE,CAAC;QACpB,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACX,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAA;QACX,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;IACb,CAAC;IAED,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;IACT,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACrB,GAAG,CAAC;QACF,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,CAAA;QAEhC,QAAQ,IAAI,EAAE,CAAC;YACb,KAAK,QAAQ;gBACX,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,QAAQ,EAAE,CAAA;gBACnC,MAAK;YAEP,KAAK,UAAU;gBACb,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,UAAU,EAAE,CAAA;gBACvC,MAAK;YAEP,KAAK,UAAU;gBACb,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,UAAU,EAAE,CAAA;gBACvC,MAAK;YAEP,KAAK,WAAW;gBACd,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC,UAAU,EAAE,CAAA;gBACtC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,QAAQ,EAAE,CAAA;gBAClC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC7B,MAAK;YAEP,KAAK,SAAS;gBACZ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,QAAQ,EAAE,CAAA;gBACrD,MAAK;YAEP,KAAK,UAAU;gBACb,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,QAAQ,EAAE,CAAA;gBACpD,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,aAAa,CAAC,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC7B,MAAK;YAEP,KAAK,SAAS;gBACZ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;gBACjB,MAAK;YAEP;gBACE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAA;gBACZ,MAAK;QACT,CAAC;QAED,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;IACnB,CAAC,QAAQ,IAAI,IAAI,OAAO,EAAC;IAEzB,OAAO,CAAC,CAAC,CAAC,CAAC,CAAA;AACb,CAAC;AAED,yEAAyE;AACzE,qEAAqE;AACrE,mCAAmC;AACnC,SAAgB,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,SAAS;IACxC,IAAI,GAAG,GAAG,IAAI,kBAAQ,CAAC,GAAG,CAAC,CAAA;IAC3B,MAAM,IAAI,GAAG,GAAG,CAAC,UAAU,EAAE,CAAA;IAC7B,MAAM,MAAM,GAAG,GAAG,CAAC,UAAU,EAAE,CAAA;IAC/B,MAAM,SAAS,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAEhC,MAAM,CAAC,GAAG,sBAAsB,CAAC,GAAG,EAAE,GAAG,EAAE,SAAS,EAAE,MAAM,CAAC,CAAA;IAC7D,MAAM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package/dist/util.d.ts

@@ -0,0 +1 @@
+export declare function concatUint8Array(args: Uint8Array[]): Uint8Array<ArrayBuffer>;

package/dist/util.js

@@ -0,0 +1,20 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.concatUint8Array = concatUint8Array;
+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;
+}
+//# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAOA,4CAQC;AAfD,SAAS,GAAG,CAAC,KAAmB;IAC9B,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,MAAM,KAAK,IAAI,KAAK,EAAE,CAAC;QAC1B,GAAG,IAAI,KAAK,CAAC,MAAM,CAAA;IACrB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AACD,SAAgB,gBAAgB,CAAC,IAAkB;IACjD,MAAM,WAAW,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,WAAW,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAC9B,MAAM,IAAI,KAAK,CAAC,MAAM,CAAA;IACxB,CAAC;IACD,OAAO,WAAW,CAAA;AACpB,CAAC"}

package/esm/cramFile/codecs/_base.d.ts

@@ -23,5 +23,5 @@ export default abstract class CramCodec<TResult extends DataType = DataType, TPa
     parameters: TParameters;
     dataType: DataType;
     constructor(parameters: TParameters, dataType: TResult);
-    abstract decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): DataTypeMapping[TResult];
+    abstract decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): DataTypeMapping[TResult] | undefined;
 }

package/esm/cramFile/codecs/byteArrayLength.js

@@ -7,11 +7,12 @@ export default class ByteArrayStopCodec extends CramCodec {
     }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const lengthCodec = this._getLengthCodec();
-        const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+        const arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
         const dataCodec = this._getDataCodec();
         const data = new Uint8Array(arrayLength);
         for (let i = 0; i < arrayLength; i += 1) {
-            data[i] = dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
+            data[i] =
+                dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors) || 0;
         }
         return data;
     }

package/esm/cramFile/codecs/byteArrayLength.js.map

@@ -1 +1 @@
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+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAK5C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAOrC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;IAC1C,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GACf,WAAW,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAE3E,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,CAAC,CAAC;gBACL,SAAS,CAAC,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO,CAAC,IAAI,CAAC,CAAA;QAC3E,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AAED,+BAA+B,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;IAC1D,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAA;AACzC,CAAC,CAAC,CAAA"}

package/esm/cramFile/codecs/external.d.ts

@@ -5,7 +5,7 @@ import { ExternalCramEncoding } from '../encoding';
 export default class ExternalCodec extends CramCodec<'int' | 'byte', ExternalCramEncoding['parameters']> {
     private readonly _decodeData;
     constructor(parameters: ExternalCramEncoding['parameters'], dataType: 'int' | 'byte');
-    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number | undefined;
     _decodeInt(contentBlock: CramFileBlock, cursor: Cursor): number;
     _decodeByte(contentBlock: CramFileBlock, cursor: Cursor): number;
 }

package/esm/cramFile/codecs/external.js

@@ -1,5 +1,5 @@
 import CramCodec from './_base';
-import { CramMalformedError, CramUnimplementedError } from '../../errors';
+import { CramUnimplementedError } from '../../errors';
 import { parseItf8 } from '../util';
 import { CramBufferOverrunError } from './getBits';
 export default class ExternalCodec extends CramCodec {
@@ -18,11 +18,8 @@ export default class ExternalCodec extends CramCodec {
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
-        if (!contentBlock) {
-            throw new CramMalformedError(`no block found with content ID ${blockContentId}}`);
-        }
         const cursor = cursors.externalBlocks.getCursor(blockContentId);
-        return this._decodeData(contentBlock, cursor);
+        return contentBlock ? this._decodeData(contentBlock, cursor) : undefined;
     }
     _decodeInt(contentBlock, cursor) {
         const [result, bytesRead] = parseItf8(contentBlock.content, cursor.bytePosition);

package/esm/cramFile/codecs/external.js.map

@@ -1 +1 @@
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+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AAGrD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AACnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QAEtD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,YAAY,CAAC,CAAC,CAAC,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IAC1E,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,SAAS,CACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAE,CAAA;IACrD,CAAC;CACF"}

package/esm/cramFile/container/index.d.ts

@@ -5,30 +5,21 @@ export default class CramContainer {
     file: CramFile;
     filePosition: number;
     constructor(file: CramFile, filePosition: number);
-    getHeader(): Promise<({
+    getHeader(): Promise<{
+        _size: number;
+        _endPosition: number;
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
         length: number;
         refSeqId: number;
         refSeqStart: number;
         alignmentSpan: number;
         numBlocks: number;
-        numLandmarks: number;
         numBases: number | undefined;
         recordCounter: number;
         numRecords: number;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        numLandmarks: number;
-        landmarks: number[];
-        crc32?: number | undefined;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        _size: number;
-        _endPosition: number;
-    }) | undefined>;
+    }>;
     getCompressionHeaderBlock(): Promise<{
         parsedContent: {
             dataSeriesEncoding: import("../codecs/dataSeriesTypes").DataSeriesEncodingMap;
@@ -48,32 +39,23 @@ export default class CramContainer {
         _size: number;
         content: Uint8Array;
         crc32?: number;
-    } | null | undefined>;
-    getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
+    } | null>;
+    getFirstBlock(): Promise<import("../file").CramFileBlock>;
     getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
     getSlice(slicePosition: number, sliceSize: number): CramSlice;
-    _readContainerHeader(position: number): Promise<({
+    _readContainerHeader(position: number): Promise<{
+        _size: number;
+        _endPosition: number;
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
         length: number;
         refSeqId: number;
         refSeqStart: number;
         alignmentSpan: number;
         numBlocks: number;
-        numLandmarks: number;
         numBases: number | undefined;
         recordCounter: number;
         numRecords: number;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        numLandmarks: number;
-        landmarks: number[];
-        crc32?: number | undefined;
-    } & {
-        _endPosition: number;
-        _size: number;
-    } & {
-        _size: number;
-        _endPosition: number;
-    }) | undefined>;
+    }>;
 }