@gmod/cram 1.6.3 → 1.7.0

package/dist/cramFile/codecs/gamma.js

@@ -1,45 +1,27 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var _base_1 = __importDefault(require("./_base"));
-var GammaCodec = /** @class */ (function (_super) {
-    __extends(GammaCodec, _super);
-    function GammaCodec(parameters, dataType) {
-        if (parameters === void 0) { parameters = {}; }
-        var _this = _super.call(this, parameters, dataType) || this;
-        if (_this.dataType !== 'int') {
-            throw new errors_1.CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by GAMMA codec"));
+const errors_1 = require("../../errors");
+const _base_1 = __importDefault(require("./_base"));
+const getBits_1 = require("./getBits");
+class GammaCodec extends _base_1.default {
+    constructor(parameters, dataType) {
+        super(parameters, dataType);
+        if (this.dataType !== 'int') {
+            throw new errors_1.CramUnimplementedError(`${this.dataType} decoding not yet implemented by GAMMA codec`);
         }
-        return _this;
     }
-    GammaCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
-        var length = 1;
-        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
-            length += 1;
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        let length = 1;
+        while ((0, getBits_1.getBits)(coreDataBlock.content, cursors.coreBlock, 1) === 0) {
+            length = length + 1;
         }
-        var readBits = this._getBits(coreDataBlock.content, cursors.coreBlock, length - 1);
-        var value = readBits | (1 << (length - 1));
+        const readBits = (0, getBits_1.getBits)(coreDataBlock.content, cursors.coreBlock, length - 1);
+        const value = readBits | (1 << (length - 1));
         return value - this.parameters.offset;
-    };
-    return GammaCodec;
-}(_base_1.default));
+    }
+}
 exports.default = GammaCodec;
 //# sourceMappingURL=gamma.js.map

package/dist/cramFile/codecs/gamma.js.map

@@ -1 +1 @@
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+{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,UAAW,SAAQ,eAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;SACF;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE;YACjE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;SACpB;QAED,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF;AAlCD,6BAkCC"}

package/dist/cramFile/codecs/getBits.d.ts

@@ -0,0 +1,7 @@
+/// <reference types="node" />
+export declare class CramBufferOverrunError extends Error {
+}
+export declare function getBits(data: Buffer, cursor: {
+    bytePosition: number;
+    bitPosition: number;
+}, numBits: number): number;

package/dist/cramFile/codecs/getBits.js

@@ -0,0 +1,26 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getBits = exports.CramBufferOverrunError = void 0;
+class CramBufferOverrunError extends Error {
+}
+exports.CramBufferOverrunError = CramBufferOverrunError;
+function getBits(data, cursor, numBits) {
+    let val = 0;
+    if (cursor.bytePosition + (7 - cursor.bitPosition + numBits) / 8 >
+        data.length) {
+        throw new CramBufferOverrunError('read error during decoding. the file seems to be truncated.');
+    }
+    for (let dlen = numBits; dlen; dlen--) {
+        // get the next `dlen` bits in the input, put them in val
+        val <<= 1;
+        val |= (data[cursor.bytePosition] >> cursor.bitPosition) & 1;
+        cursor.bitPosition -= 1;
+        if (cursor.bitPosition < 0) {
+            cursor.bytePosition += 1;
+        }
+        cursor.bitPosition &= 7;
+    }
+    return val;
+}
+exports.getBits = getBits;
+//# sourceMappingURL=getBits.js.map

package/dist/cramFile/codecs/getBits.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAAA,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,SAAgB,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX;QACA,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;KACF;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE;QACrC,yDAAyD;QACzD,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC5D,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE;YAC1B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;SACzB;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;KACxB;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAzBD,0BAyBC"}

package/dist/cramFile/codecs/huffman.d.ts

@@ -1,17 +1,21 @@
-export default class HuffmanIntCodec extends CramCodec {
-    _decode(slice: any, coreDataBlock: any, coreCursor: any): any;
+import CramCodec, { Cursor, Cursors } from './_base';
+import { HuffmanEncoding } from '../encoding';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEncoding['parameters']> {
+    private codes;
+    private codeBook;
+    private sortedByValue;
+    private sortedCodes;
+    private sortedValuesByBitCode;
+    private sortedBitCodes;
+    private sortedBitLengthsByBitCode;
+    private bitCodeToValue;
+    constructor(parameters: HuffmanEncoding['parameters'], dataType: 'byte' | 'int');
     buildCodeBook(): void;
-    codeBook: {} | undefined;
     buildCodes(): void;
-    codes: {} | undefined;
     buildCaches(): void;
-    sortedCodes: any[] | undefined;
-    sortedByValue: any[] | undefined;
-    sortedValuesByBitCode: any[] | undefined;
-    sortedBitCodes: any[] | undefined;
-    sortedBitLengthsByBitCode: any[] | undefined;
-    bitCodeToValue: any[] | undefined;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any;
-    _decodeZeroLengthCode(): any;
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
+    _decodeZeroLengthCode(): number;
+    _decode(slice: CramSlice, coreDataBlock: CramFileBlock, coreCursor: Cursor): number;
 }
-import CramCodec from "./_base";

package/dist/cramFile/codecs/huffman.js

@@ -1,135 +1,126 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var _base_1 = __importDefault(require("./_base"));
+const errors_1 = require("../../errors");
+const _base_1 = __importDefault(require("./_base"));
+const getBits_1 = require("./getBits");
 function numberOfSetBits(ii) {
-    var i = (ii - (ii >> 1)) & 0x55555555;
+    let i = (ii - (ii >> 1)) & 0x55555555;
     i = (i & 0x33333333) + ((i >> 2) & 0x33333333);
     return (((i + (i >> 4)) & 0x0f0f0f0f) * 0x01010101) >> 24;
 }
-var HuffmanIntCodec = /** @class */ (function (_super) {
-    __extends(HuffmanIntCodec, _super);
-    function HuffmanIntCodec(parameters, dataType) {
-        if (parameters === void 0) { parameters = {}; }
-        var _this = _super.call(this, parameters, dataType) || this;
-        if (!['byte', 'int'].includes(_this.dataType)) {
-            throw new TypeError("".concat(_this.dataType, " decoding not yet implemented by HUFFMAN_INT codec"));
+class HuffmanIntCodec extends _base_1.default {
+    constructor(parameters, dataType) {
+        super(parameters, dataType);
+        this.codes = {};
+        this.codeBook = {};
+        this.sortedByValue = [];
+        this.sortedCodes = [];
+        this.sortedValuesByBitCode = [];
+        this.sortedBitCodes = [];
+        this.sortedBitLengthsByBitCode = [];
+        this.bitCodeToValue = [];
+        if (!['byte', 'int'].includes(this.dataType)) {
+            throw new TypeError(`${this.dataType} decoding not yet implemented by HUFFMAN_INT codec`);
         }
-        _this.buildCodeBook();
-        _this.buildCodes();
-        _this.buildCaches();
+        this.buildCodeBook();
+        this.buildCodes();
+        this.buildCaches();
         // if this is a degenerate zero-length huffman code, special-case the decoding
-        if (_this.sortedCodes[0].bitLength === 0) {
-            _this._decode = _this._decodeZeroLengthCode;
+        if (this.sortedCodes[0].bitLength === 0) {
+            this._decode = this._decodeZeroLengthCode;
         }
-        return _this;
     }
-    HuffmanIntCodec.prototype.buildCodeBook = function () {
-        var _this = this;
+    buildCodeBook() {
         // parse the parameters together into a `codes` data structure
-        var codes = new Array(this.parameters.numCodes);
-        for (var i = 0; i < this.parameters.numCodes; i += 1) {
+        let codes = new Array(this.parameters.numCodes);
+        for (let i = 0; i < this.parameters.numCodes; i += 1) {
             codes[i] = {
                 symbol: this.parameters.symbols[i],
                 bitLength: this.parameters.bitLengths[i],
             };
         }
         // sort the codes by bit length and symbol value
-        codes = codes.sort(function (a, b) { return a.bitLength - b.bitLength || a.symbol - b.symbol; });
+        codes = codes.sort((a, b) => a.bitLength - b.bitLength || a.symbol - b.symbol);
         this.codeBook = {};
-        codes.forEach(function (code) {
-            if (!_this.codeBook[code.bitLength]) {
-                _this.codeBook[code.bitLength] = [];
+        codes.forEach(code => {
+            if (!this.codeBook[code.bitLength]) {
+                this.codeBook[code.bitLength] = [];
             }
-            _this.codeBook[code.bitLength].push(code.symbol);
+            this.codeBook[code.bitLength].push(code.symbol);
         });
-    };
-    HuffmanIntCodec.prototype.buildCodes = function () {
-        var _this = this;
+    }
+    buildCodes() {
         this.codes = {}; /*  new TreeMap<Integer, HuffmanBitCode>(); */
-        var codeLength = 0;
-        var codeValue = -1;
-        Object.entries(this.codeBook).forEach(function (_a) {
-            var bitLength = _a[0], symbols = _a[1];
-            bitLength = parseInt(bitLength, 10);
-            symbols.forEach(function (symbol) {
-                var code = { bitLength: bitLength, value: symbol };
-                codeValue += 1;
-                var delta = bitLength - codeLength; // new length?
-                codeValue <<= delta; // pad with 0's
+        let codeLength = 0;
+        let codeValue = -1;
+        Object.entries(this.codeBook).forEach(([bitLength, symbols]) => {
+            const bitLengthInt = parseInt(bitLength, 10);
+            symbols.forEach(symbol => {
+                const code = {
+                    bitLength: bitLengthInt,
+                    value: symbol,
+                    bitCode: 0,
+                };
+                codeValue = codeValue + 1;
+                const delta = bitLengthInt - codeLength; // new length?
+                codeValue = codeValue << delta; // pad with 0's
                 code.bitCode = codeValue; // calculated: huffman code
-                codeLength += delta; // adjust current code length
-                if (numberOfSetBits(codeValue) > bitLength) {
+                codeLength = codeLength + delta; // adjust current code length
+                if (numberOfSetBits(codeValue) > bitLengthInt) {
                     throw new errors_1.CramMalformedError('Symbol out of range');
                 }
-                _this.codes[symbol] = code;
+                this.codes[symbol] = code;
             });
         });
-    };
-    HuffmanIntCodec.prototype.buildCaches = function () {
-        this.sortedCodes = Object.values(this.codes).sort(function (a, b) { return a.bitLength - b.bitLength || a.bitCode - b.bitCode; });
+    }
+    buildCaches() {
+        this.sortedCodes = Object.values(this.codes).sort((a, b) => a.bitLength - b.bitLength || a.bitCode - b.bitCode);
         // this.sortedValues = this.parameters.values.sort((a,b) => a-b)
-        this.sortedByValue = Object.values(this.codes).sort(function (a, b) { return a.value - b.value; });
-        this.sortedValuesByBitCode = this.sortedCodes.map(function (c) { return c.value; });
-        this.sortedBitCodes = this.sortedCodes.map(function (c) { return c.bitCode; });
-        this.sortedBitLengthsByBitCode = this.sortedCodes.map(function (c) { return c.bitLength; });
-        var maxBitCode = Math.max.apply(Math, this.sortedBitCodes);
+        this.sortedByValue = Object.values(this.codes).sort((a, b) => a.value - b.value);
+        this.sortedValuesByBitCode = this.sortedCodes.map(c => c.value);
+        this.sortedBitCodes = this.sortedCodes.map(c => c.bitCode);
+        this.sortedBitLengthsByBitCode = this.sortedCodes.map(c => c.bitLength);
+        const maxBitCode = Math.max(...this.sortedBitCodes);
         this.bitCodeToValue = new Array(maxBitCode + 1).fill(-1);
-        for (var i = 0; i < this.sortedBitCodes.length; i += 1) {
+        for (let i = 0; i < this.sortedBitCodes.length; i += 1) {
             this.bitCodeToValue[this.sortedCodes[i].bitCode] = i;
         }
-    };
-    HuffmanIntCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
+    }
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
         return this._decode(slice, coreDataBlock, cursors.coreBlock);
-    };
+    }
     // _decodeNull() {
     //   return -1
     // }
     // the special case for zero-length codes
-    HuffmanIntCodec.prototype._decodeZeroLengthCode = function () {
+    _decodeZeroLengthCode() {
         return this.sortedCodes[0].value;
-    };
-    HuffmanIntCodec.prototype._decode = function (slice, coreDataBlock, coreCursor) {
-        var input = coreDataBlock.content;
-        var prevLen = 0;
-        var bits = 0;
-        for (var i = 0; i < this.sortedCodes.length; i += 1) {
-            var length_1 = this.sortedCodes[i].bitLength;
-            bits <<= length_1 - prevLen;
-            bits |= this._getBits(input, coreCursor, length_1 - prevLen);
-            prevLen = length_1;
+    }
+    _decode(slice, coreDataBlock, coreCursor) {
+        const input = coreDataBlock.content;
+        let prevLen = 0;
+        let bits = 0;
+        for (let i = 0; i < this.sortedCodes.length; i += 1) {
+            const length = this.sortedCodes[i].bitLength;
+            bits <<= length - prevLen;
+            bits |= (0, getBits_1.getBits)(input, coreCursor, length - prevLen);
+            prevLen = length;
             {
-                var index = this.bitCodeToValue[bits];
-                if (index > -1 && this.sortedBitLengthsByBitCode[index] === length_1) {
+                const index = this.bitCodeToValue[bits];
+                if (index > -1 && this.sortedBitLengthsByBitCode[index] === length) {
                     return this.sortedValuesByBitCode[index];
                 }
-                for (var j = i; this.sortedCodes[j + 1].bitLength === length_1 &&
+                for (let j = i; this.sortedCodes[j + 1].bitLength === length &&
                     j < this.sortedCodes.length; j += 1) {
                     i += 1;
                 }
             }
         }
         throw new errors_1.CramMalformedError('Huffman symbol not found.');
-    };
-    return HuffmanIntCodec;
-}(_base_1.default));
+    }
+}
 exports.default = HuffmanIntCodec;
 //# sourceMappingURL=huffman.js.map

package/dist/cramFile/codecs/huffman.js.map

@@ -1 +1 @@
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+{"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":";;;;;AAAA,yCAAiD;AACjD,oDAAoD;AACpD,uCAAmC;AAMnC,SAAS,eAAe,CAAC,EAAU;IACjC,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAA;IACrC,CAAC,GAAG,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,UAAU,CAAC,CAAA;IAC9C,OAAO,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,UAAU,CAAC,IAAI,EAAE,CAAA;AAC3D,CAAC;AAID,MAAqB,eAAgB,SAAQ,eAG5C;IAUC,YACE,UAAyC,EACzC,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAbrB,UAAK,GAAyB,EAAE,CAAA;QAChC,aAAQ,GAA6B,EAAE,CAAA;QACvC,kBAAa,GAAW,EAAE,CAAA;QAC1B,gBAAW,GAAW,EAAE,CAAA;QACxB,0BAAqB,GAAa,EAAE,CAAA;QACpC,mBAAc,GAAa,EAAE,CAAA;QAC7B,8BAAyB,GAAa,EAAE,CAAA;QACxC,mBAAc,GAAa,EAAE,CAAA;QAOnC,IAAI,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE;YAC5C,MAAM,IAAI,SAAS,CACjB,GAAG,IAAI,CAAC,QAAQ,oDAAoD,CACrE,CAAA;SACF;QAED,IAAI,CAAC,aAAa,EAAE,CAAA;QACpB,IAAI,CAAC,UAAU,EAAE,CAAA;QACjB,IAAI,CAAC,WAAW,EAAE,CAAA;QAElB,8EAA8E;QAC9E,IAAI,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,KAAK,CAAC,EAAE;YACvC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,qBAAqB,CAAA;SAC1C;IACH,CAAC;IAED,aAAa;QACX,8DAA8D;QAC9D,IAAI,KAAK,GAAiD,IAAI,KAAK,CACjE,IAAI,CAAC,UAAU,CAAC,QAAQ,CACzB,CAAA;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;YACpD,KAAK,CAAC,CAAC,CAAC,GAAG;gBACT,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC;gBAClC,SAAS,EAAE,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC,CAAC;aACzC,CAAA;SACF;QACD,gDAAgD;QAChD,KAAK,GAAG,KAAK,CAAC,IAAI,CAChB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAC3D,CAAA;QAED,IAAI,CAAC,QAAQ,GAAG,EAAE,CAAA;QAClB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;YACnB,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE;gBAClC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,CAAA;aACnC;YACD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACjD,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,UAAU;QACR,IAAI,CAAC,KAAK,GAAG,EAAE,CAAA,CAAC,8CAA8C;QAC9D,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,IAAI,SAAS,GAAG,CAAC,CAAC,CAAA;QAClB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE;YAC7D,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,EAAE,EAAE,CAAC,CAAA;YAC5C,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;gBACvB,MAAM,IAAI,GAAG;oBACX,SAAS,EAAE,YAAY;oBACvB,KAAK,EAAE,MAAM;oBACb,OAAO,EAAE,CAAC;iBACX,CAAA;gBACD,SAAS,GAAG,SAAS,GAAG,CAAC,CAAA;gBACzB,MAAM,KAAK,GAAG,YAAY,GAAG,UAAU,CAAA,CAAC,cAAc;gBACtD,SAAS,GAAG,SAAS,IAAI,KAAK,CAAA,CAAC,eAAe;gBAC9C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA,CAAC,2BAA2B;gBACpD,UAAU,GAAG,UAAU,GAAG,KAAK,CAAA,CAAC,6BAA6B;gBAE7D,IAAI,eAAe,CAAC,SAAS,CAAC,GAAG,YAAY,EAAE;oBAC7C,MAAM,IAAI,2BAAkB,CAAC,qBAAqB,CAAC,CAAA;iBACpD;gBAED,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,IAAI,CAAA;YAC3B,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,WAAW;QACT,IAAI,CAAC,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAC/C,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAC7D,CAAA;QAED,gEAAgE;QAChE,IAAI,CAAC,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CACjD,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,CAC5B,CAAA;QAED,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;QAC/D,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;QAC1D,IAAI,CAAC,yBAAyB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAA;QACvE,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,CAAA;QAEnD,IAAI,CAAC,cAAc,GAAG,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YACtD,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;SACrD;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,aAAa,EAAE,OAAO,CAAC,SAAS,CAAC,CAAA;IAC9D,CAAC;IAED,kBAAkB;IAClB,cAAc;IACd,IAAI;IAEJ,yCAAyC;IACzC,qBAAqB;QACnB,OAAO,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;IAClC,CAAC;IAED,OAAO,CAAC,KAAgB,EAAE,aAA4B,EAAE,UAAkB;QACxE,MAAM,KAAK,GAAG,aAAa,CAAC,OAAO,CAAA;QAEnC,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YACnD,MAAM,MAAM,GAAG,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YAC5C,IAAI,KAAK,MAAM,GAAG,OAAO,CAAA;YACzB,IAAI,IAAI,IAAA,iBAAO,EAAC,KAAK,EAAE,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,CAAA;YACpD,OAAO,GAAG,MAAM,CAAA;YAChB;gBACE,MAAM,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;gBACvC,IAAI,KAAK,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,yBAAyB,CAAC,KAAK,CAAC,KAAK,MAAM,EAAE;oBAClE,OAAO,IAAI,CAAC,qBAAqB,CAAC,KAAK,CAAC,CAAA;iBACzC;gBAED,KACE,IAAI,CAAC,GAAG,CAAC,EACT,IAAI,CAAC,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,KAAK,MAAM;oBAC5C,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,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package/dist/cramFile/codecs/index.d.ts

@@ -1,2 +1,4 @@
-export function getCodecClassWithId(id: any): any;
-export function instantiateCodec(encodingData: any, dataType: any): any;
+import CramCodec from './_base';
+import { CramEncoding } from '../encoding';
+import { DataType } from './dataSeriesTypes';
+export declare function instantiateCodec<TResult extends DataType = DataType>(encodingData: CramEncoding, dataType: DataType | 'ignore'): CramCodec<TResult>;

package/dist/cramFile/codecs/index.js

@@ -3,16 +3,16 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.instantiateCodec = exports.getCodecClassWithId = void 0;
-var errors_1 = require("../../errors");
-var huffman_1 = __importDefault(require("./huffman"));
-var external_1 = __importDefault(require("./external"));
-var byteArrayStop_1 = __importDefault(require("./byteArrayStop"));
-var byteArrayLength_1 = __importDefault(require("./byteArrayLength"));
-var beta_1 = __importDefault(require("./beta"));
-var gamma_1 = __importDefault(require("./gamma"));
-var subexp_1 = __importDefault(require("./subexp"));
-var codecClasses = {
+exports.instantiateCodec = void 0;
+const errors_1 = require("../../errors");
+const huffman_1 = __importDefault(require("./huffman"));
+const external_1 = __importDefault(require("./external"));
+const byteArrayStop_1 = __importDefault(require("./byteArrayStop"));
+const byteArrayLength_1 = __importDefault(require("./byteArrayLength"));
+const beta_1 = __importDefault(require("./beta"));
+const gamma_1 = __importDefault(require("./gamma"));
+const subexp_1 = __importDefault(require("./subexp"));
+const codecClasses = {
     1: external_1.default,
     // 2: GolombCodec,
     3: huffman_1.default,
@@ -26,11 +26,10 @@ var codecClasses = {
 function getCodecClassWithId(id) {
     return codecClasses[id];
 }
-exports.getCodecClassWithId = getCodecClassWithId;
 function instantiateCodec(encodingData, dataType) {
-    var CodecClass = getCodecClassWithId(dataType === 'ignore' ? 0 : encodingData.codecId);
+    const CodecClass = getCodecClassWithId(dataType === 'ignore' ? 0 : encodingData.codecId);
     if (!CodecClass) {
-        throw new errors_1.CramUnimplementedError("no codec implemented for codec ID ".concat(encodingData.codecId));
+        throw new errors_1.CramUnimplementedError(`no codec implemented for codec ID ${encodingData.codecId}`);
     }
     return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
 }

package/dist/cramFile/codecs/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":";;;;;;AAAA,yCAAqD;AAErD,wDAAuC;AACvC,0DAAsC;AACtC,oEAAgD;AAChD,wEAAoD;AACpD,kDAA8B;AAC9B,oDAAgC;AAChC,sDAAkC;AAKlC,MAAM,YAAY,GAAG;IACnB,CAAC,EAAE,kBAAa;IAChB,kBAAkB;IAClB,CAAC,EAAE,iBAAe;IAClB,CAAC,EAAE,yBAAoB;IACvB,CAAC,EAAE,uBAAkB;IACrB,CAAC,EAAE,cAAS;IACZ,CAAC,EAAE,gBAAW;IACd,sBAAsB;IACtB,CAAC,EAAE,eAAU;CACd,CAAA;AAED,SAAS,mBAAmB,CAAC,EAAU;IACrC,OAAQ,YAAoB,CAAC,EAAE,CAAC,CAAA;AAClC,CAAC;AAED,SAAgB,gBAAgB,CAC9B,YAA0B,EAC1B,QAA6B;IAE7B,MAAM,UAAU,GAAG,mBAAmB,CACpC,QAAQ,KAAK,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,OAAO,CACjD,CAAA;IACD,IAAI,CAAC,UAAU,EAAE;QACf,MAAM,IAAI,+BAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;KACF;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC;AAdD,4CAcC"}

package/dist/cramFile/codecs/subexp.d.ts

@@ -1,4 +1,8 @@
-export default class SubexpCodec extends CramCodec {
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): number;
+import CramCodec, { Cursors } from './_base';
+import CramSlice from '../slice';
+import { CramFileBlock } from '../file';
+import { SubexpEncoding } from '../encoding';
+export default class SubexpCodec extends CramCodec<'int', SubexpEncoding['parameters']> {
+    constructor(parameters: SubexpEncoding['parameters'], dataType: 'int');
+    decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): number;
 }
-import CramCodec from "./_base";

package/dist/cramFile/codecs/subexp.js

@@ -1,53 +1,36 @@
 "use strict";
-var __extends = (this && this.__extends) || (function () {
-    var extendStatics = function (d, b) {
-        extendStatics = Object.setPrototypeOf ||
-            ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||
-            function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };
-        return extendStatics(d, b);
-    };
-    return function (d, b) {
-        if (typeof b !== "function" && b !== null)
-            throw new TypeError("Class extends value " + String(b) + " is not a constructor or null");
-        extendStatics(d, b);
-        function __() { this.constructor = d; }
-        d.prototype = b === null ? Object.create(b) : (__.prototype = b.prototype, new __());
-    };
-})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var _base_1 = __importDefault(require("./_base"));
-var SubexpCodec = /** @class */ (function (_super) {
-    __extends(SubexpCodec, _super);
-    function SubexpCodec(parameters, dataType) {
-        if (parameters === void 0) { parameters = {}; }
-        var _this = _super.call(this, parameters, dataType) || this;
-        if (_this.dataType !== 'int') {
-            throw new errors_1.CramUnimplementedError("".concat(_this.dataType, " decoding not yet implemented by SUBEXP codec"));
+const errors_1 = require("../../errors");
+const _base_1 = __importDefault(require("./_base"));
+const getBits_1 = require("./getBits");
+class SubexpCodec extends _base_1.default {
+    constructor(parameters, dataType) {
+        super(parameters, dataType);
+        if (this.dataType !== 'int') {
+            throw new errors_1.CramUnimplementedError(`${this.dataType} decoding not yet implemented by SUBEXP codec`);
         }
-        return _this;
     }
-    SubexpCodec.prototype.decode = function (slice, coreDataBlock, blocksByContentId, cursors) {
-        var numLeadingOnes = 0;
-        while (this._getBits(coreDataBlock.content, cursors.coreBlock, 1)) {
-            numLeadingOnes += 1;
+    decode(slice, coreDataBlock, blocksByContentId, cursors) {
+        let numLeadingOnes = 0;
+        while ((0, getBits_1.getBits)(coreDataBlock.content, cursors.coreBlock, 1)) {
+            numLeadingOnes = numLeadingOnes + 1;
         }
-        var b;
-        var n;
+        let b;
+        let n;
         if (numLeadingOnes === 0) {
             b = this.parameters.K;
-            n = this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+            n = (0, getBits_1.getBits)(coreDataBlock.content, cursors.coreBlock, b);
         }
         else {
             b = numLeadingOnes + this.parameters.K - 1;
-            n = (1 << b) | this._getBits(coreDataBlock.content, cursors.coreBlock, b);
+            const bits = (0, getBits_1.getBits)(coreDataBlock.content, cursors.coreBlock, b);
+            n = (1 << b) | bits;
         }
         return n - this.parameters.offset;
-    };
-    return SubexpCodec;
-}(_base_1.default));
+    }
+}
 exports.default = SubexpCodec;
 //# sourceMappingURL=subexp.js.map

package/dist/cramFile/codecs/subexp.js.map

@@ -1 +1 @@
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+{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,WAAY,SAAQ,eAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;SACF;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE;YAC3D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;SACpC;QAED,IAAI,CAAC,CAAA;QACL,IAAI,CAAC,CAAA;QACL,IAAI,cAAc,KAAK,CAAC,EAAE;YACxB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;SACzD;aAAM;YACL,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;SACpB;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF;AArCD,8BAqCC"}

package/dist/cramFile/constants.d.ts

@@ -1,36 +1,36 @@
+declare const Constants: {
+    CRAM_FLAG_PRESERVE_QUAL_SCORES: number;
+    CRAM_FLAG_DETACHED: number;
+    CRAM_FLAG_MATE_DOWNSTREAM: number;
+    CRAM_FLAG_NO_SEQ: number;
+    CRAM_FLAG_MASK: number;
+    CRAM_M_REVERSE: number;
+    CRAM_M_UNMAP: number;
+    BAM_FPAIRED: number;
+    BAM_FPROPER_PAIR: number;
+    BAM_FUNMAP: number;
+    BAM_FMUNMAP: number;
+    BAM_FREVERSE: number;
+    BAM_FMREVERSE: number;
+    BAM_FREAD1: number;
+    BAM_FREAD2: number;
+    BAM_FSECONDARY: number;
+    BAM_FQCFAIL: number;
+    BAM_FDUP: number;
+    BAM_FSUPPLEMENTARY: number;
+    BAM_CMATCH: number;
+    BAM_CINS: number;
+    BAM_CDEL: number;
+    BAM_CREF_SKIP: number;
+    BAM_CSOFT_CLIP: number;
+    BAM_CHARD_CLIP: number;
+    BAM_CPAD: number;
+    BAM_CEQUAL: number;
+    BAM_CDIFF: number;
+    BAM_CBACK: number;
+    BAM_CIGAR_STR: string;
+    BAM_CIGAR_SHIFT: number;
+    BAM_CIGAR_MASK: number;
+    BAM_CIGAR_TYPE: number;
+};
 export default Constants;
-declare namespace Constants {
-    const CRAM_FLAG_PRESERVE_QUAL_SCORES: number;
-    const CRAM_FLAG_DETACHED: number;
-    const CRAM_FLAG_MATE_DOWNSTREAM: number;
-    const CRAM_FLAG_NO_SEQ: number;
-    const CRAM_FLAG_MASK: number;
-    const CRAM_M_REVERSE: number;
-    const CRAM_M_UNMAP: number;
-    const BAM_FPAIRED: number;
-    const BAM_FPROPER_PAIR: number;
-    const BAM_FUNMAP: number;
-    const BAM_FMUNMAP: number;
-    const BAM_FREVERSE: number;
-    const BAM_FMREVERSE: number;
-    const BAM_FREAD1: number;
-    const BAM_FREAD2: number;
-    const BAM_FSECONDARY: number;
-    const BAM_FQCFAIL: number;
-    const BAM_FDUP: number;
-    const BAM_FSUPPLEMENTARY: number;
-    const BAM_CMATCH: number;
-    const BAM_CINS: number;
-    const BAM_CDEL: number;
-    const BAM_CREF_SKIP: number;
-    const BAM_CSOFT_CLIP: number;
-    const BAM_CHARD_CLIP: number;
-    const BAM_CPAD: number;
-    const BAM_CEQUAL: number;
-    const BAM_CDIFF: number;
-    const BAM_CBACK: number;
-    const BAM_CIGAR_STR: string;
-    const BAM_CIGAR_SHIFT: number;
-    const BAM_CIGAR_MASK: number;
-    const BAM_CIGAR_TYPE: number;
-}

package/dist/cramFile/constants.js

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var Constants = {
+const Constants = {
     CRAM_FLAG_PRESERVE_QUAL_SCORES: 1 << 0,
     CRAM_FLAG_DETACHED: 1 << 1,
     CRAM_FLAG_MATE_DOWNSTREAM: 1 << 2,