@gmod/cram 1.6.3 → 1.7.0

package/dist/cramFile/constants.js.map

@@ -1 +1 @@
-{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/cramFile/constants.js"],"names":[],"mappings":";;AAAA,IAAM,SAAS,GAAG;IAChB,8BAA8B,EAAE,CAAC,IAAI,CAAC;IACtC,kBAAkB,EAAE,CAAC,IAAI,CAAC;IAC1B,yBAAyB,EAAE,CAAC,IAAI,CAAC;IACjC,gBAAgB,EAAE,CAAC,IAAI,CAAC;IACxB,cAAc,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC;IAE5B,wBAAwB;IACxB,cAAc,EAAE,CAAC;IACjB,yBAAyB;IACzB,YAAY,EAAE,CAAC;IAEf,8EAA8E;IAC9E,WAAW,EAAE,CAAC;IACd,uCAAuC;IACvC,gBAAgB,EAAE,CAAC;IACnB,kEAAkE;IAClE,UAAU,EAAE,CAAC;IACb,wBAAwB;IACxB,WAAW,EAAE,CAAC;IACd,4CAA4C;IAC5C,YAAY,EAAE,EAAE;IAChB,4CAA4C;IAC5C,aAAa,EAAE,EAAE;IACjB,iBAAiB;IACjB,UAAU,EAAE,EAAE;IACd,iBAAiB;IACjB,UAAU,EAAE,GAAG;IACf,yBAAyB;IACzB,cAAc,EAAE,GAAG;IACnB,cAAc;IACd,WAAW,EAAE,GAAG;IAChB,4BAA4B;IAC5B,QAAQ,EAAE,IAAI;IACd,2BAA2B;IAC3B,kBAAkB,EAAE,IAAI;IAExB,UAAU,EAAE,CAAC;IACb,QAAQ,EAAE,CAAC;IACX,QAAQ,EAAE,CAAC;IACX,aAAa,EAAE,CAAC;IAChB,cAAc,EAAE,CAAC;IACjB,cAAc,EAAE,CAAC;IACjB,QAAQ,EAAE,CAAC;IACX,UAAU,EAAE,CAAC;IACb,SAAS,EAAE,CAAC;IACZ,SAAS,EAAE,CAAC;IAEZ,aAAa,EAAE,YAAY;IAC3B,eAAe,EAAE,CAAC;IAClB,cAAc,EAAE,GAAG;IACnB,cAAc,EAAE,OAAO;CACxB,CAAA;AAED,kBAAe,SAAS,CAAA"}
+{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/cramFile/constants.ts"],"names":[],"mappings":";;AAAA,MAAM,SAAS,GAAG;IAChB,8BAA8B,EAAE,CAAC,IAAI,CAAC;IACtC,kBAAkB,EAAE,CAAC,IAAI,CAAC;IAC1B,yBAAyB,EAAE,CAAC,IAAI,CAAC;IACjC,gBAAgB,EAAE,CAAC,IAAI,CAAC;IACxB,cAAc,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC;IAE5B,wBAAwB;IACxB,cAAc,EAAE,CAAC;IACjB,yBAAyB;IACzB,YAAY,EAAE,CAAC;IAEf,8EAA8E;IAC9E,WAAW,EAAE,CAAC;IACd,uCAAuC;IACvC,gBAAgB,EAAE,CAAC;IACnB,kEAAkE;IAClE,UAAU,EAAE,CAAC;IACb,wBAAwB;IACxB,WAAW,EAAE,CAAC;IACd,4CAA4C;IAC5C,YAAY,EAAE,EAAE;IAChB,4CAA4C;IAC5C,aAAa,EAAE,EAAE;IACjB,iBAAiB;IACjB,UAAU,EAAE,EAAE;IACd,iBAAiB;IACjB,UAAU,EAAE,GAAG;IACf,yBAAyB;IACzB,cAAc,EAAE,GAAG;IACnB,cAAc;IACd,WAAW,EAAE,GAAG;IAChB,4BAA4B;IAC5B,QAAQ,EAAE,IAAI;IACd,2BAA2B;IAC3B,kBAAkB,EAAE,IAAI;IAExB,UAAU,EAAE,CAAC;IACb,QAAQ,EAAE,CAAC;IACX,QAAQ,EAAE,CAAC;IACX,aAAa,EAAE,CAAC;IAChB,cAAc,EAAE,CAAC;IACjB,cAAc,EAAE,CAAC;IACjB,QAAQ,EAAE,CAAC;IACX,UAAU,EAAE,CAAC;IACb,SAAS,EAAE,CAAC;IACZ,SAAS,EAAE,CAAC;IAEZ,aAAa,EAAE,YAAY;IAC3B,eAAe,EAAE,CAAC;IAClB,cAAc,EAAE,GAAG;IACnB,cAAc,EAAE,OAAO;CACxB,CAAA;AAED,kBAAe,SAAS,CAAA"}

package/dist/cramFile/container/compressionScheme.d.ts

@@ -1,23 +1,69 @@
+import CramCodec from '../codecs/_base';
+import { CramCompressionHeader } from '../sectionParsers';
+import { CramEncoding } from '../encoding';
+import { DataSeriesEncodingKey, DataSeriesEncodingMap } from '../codecs/dataSeriesTypes';
+declare const dataSeriesTypes: {
+    readonly BF: "int";
+    readonly CF: "int";
+    readonly RI: "int";
+    readonly RL: "int";
+    readonly AP: "int";
+    readonly RG: "int";
+    readonly MF: "int";
+    readonly NS: "int";
+    readonly NP: "int";
+    readonly TS: "int";
+    readonly NF: "int";
+    readonly TC: "byte";
+    readonly TN: "int";
+    readonly FN: "int";
+    readonly FC: "byte";
+    readonly FP: "int";
+    readonly BS: "byte";
+    readonly IN: "byteArray";
+    readonly SC: "byteArray";
+    readonly DL: "int";
+    readonly BA: "byte";
+    readonly BB: "byteArray";
+    readonly RS: "int";
+    readonly PD: "int";
+    readonly HC: "int";
+    readonly MQ: "int";
+    readonly RN: "byteArray";
+    readonly QS: "byte";
+    readonly QQ: "byteArray";
+    readonly TL: "int";
+};
+export declare type DataSeriesTypes = typeof dataSeriesTypes;
+declare type DataSeriesCache = {
+    [K in DataSeriesEncodingKey]?: CramCodec<DataSeriesTypes[K]>;
+};
 export default class CramContainerCompressionScheme {
-    constructor(content: any);
-    readNamesIncluded: any;
-    APdelta: any;
+    readNamesIncluded: boolean;
+    APdelta: boolean;
     referenceRequired: boolean;
-    tagIdsDictionary: any;
-    substitutionMatrix: any[];
-    dataSeriesCodecCache: Map<any, any>;
-    tagCodecCache: {};
+    tagIdsDictionary: Record<number, string[]>;
+    substitutionMatrix: string[][];
+    dataSeriesCodecCache: DataSeriesCache;
+    tagCodecCache: Record<string, CramCodec>;
+    tagEncoding: Record<string, CramEncoding>;
+    dataSeriesEncoding: DataSeriesEncodingMap;
+    private preservation;
+    private _endPosition;
+    private _size;
+    constructor(content: CramCompressionHeader);
     /**
      * @param {string} tagName three-character tag name
      * @private
      */
-    private getCodecForTag;
+    getCodecForTag(tagName: string): CramCodec;
     /**
      *
      * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
      * @private
      */
-    private getTagNames;
-    getCodecForDataSeries(dataSeriesName: any): any;
-    toJSON(): {};
+    getTagNames(tagListId: number): string[];
+    getCodecForDataSeries<TDataSeries extends DataSeriesEncodingKey>(dataSeriesName: TDataSeries): CramCodec<DataSeriesTypes[TDataSeries]> | undefined;
+    toJSON(): any;
 }
+export {};

package/dist/cramFile/container/compressionScheme.js

@@ -1,10 +1,10 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-var errors_1 = require("../../errors");
-var codecs_1 = require("../codecs");
+const codecs_1 = require("../codecs");
+const errors_1 = require("../../errors");
 // the hardcoded data type to be decoded for each core
 // data field
-var dataSeriesTypes = {
+const dataSeriesTypes = {
     BF: 'int',
     CF: 'int',
     RI: 'int',
@@ -35,12 +35,12 @@ var dataSeriesTypes = {
     QS: 'byte',
     QQ: 'byteArray',
     TL: 'int',
-    TM: 'ignore',
-    TV: 'ignore',
+    // TM: 'ignore',
+    // TV: 'ignore',
 };
 function parseSubstitutionMatrix(byteArray) {
-    var matrix = new Array(5);
-    for (var i = 0; i < 5; i += 1) {
+    const matrix = new Array(5);
+    for (let i = 0; i < 5; i += 1) {
         matrix[i] = new Array(4);
     }
     matrix[0][(byteArray[0] >> 6) & 3] = 'C';
@@ -65,66 +65,71 @@ function parseSubstitutionMatrix(byteArray) {
     matrix[4][(byteArray[4] >> 0) & 3] = 'T';
     return matrix;
 }
-var CramContainerCompressionScheme = /** @class */ (function () {
-    function CramContainerCompressionScheme(content) {
-        Object.assign(this, content);
+class CramContainerCompressionScheme {
+    constructor(content) {
+        this.dataSeriesCodecCache = {};
+        this.tagCodecCache = {};
+        this.tagEncoding = {};
+        // Object.assign(this, content)
         // interpret some of the preservation map tags for convenient use
         this.readNamesIncluded = content.preservation.RN;
         this.APdelta = content.preservation.AP;
         this.referenceRequired = !!content.preservation.RR;
         this.tagIdsDictionary = content.preservation.TD;
         this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
-        this.dataSeriesCodecCache = new Map();
-        this.tagCodecCache = {};
+        this.dataSeriesEncoding = content.dataSeriesEncoding;
+        this.tagEncoding = content.tagEncoding;
+        this.preservation = content.preservation;
+        this._size = content._size;
+        this._endPosition = content._endPosition;
     }
     /**
      * @param {string} tagName three-character tag name
      * @private
      */
-    CramContainerCompressionScheme.prototype.getCodecForTag = function (tagName) {
+    getCodecForTag(tagName) {
         if (!this.tagCodecCache[tagName]) {
-            var encodingData = this.tagEncoding[tagName];
+            const encodingData = this.tagEncoding[tagName];
             if (encodingData) {
                 this.tagCodecCache[tagName] = (0, codecs_1.instantiateCodec)(encodingData, 'byteArray');
             }
         }
         return this.tagCodecCache[tagName];
-    };
+    }
     /**
      *
      * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
      * @private
      */
-    CramContainerCompressionScheme.prototype.getTagNames = function (tagListId) {
+    getTagNames(tagListId) {
         return this.tagIdsDictionary[tagListId];
-    };
-    CramContainerCompressionScheme.prototype.getCodecForDataSeries = function (dataSeriesName) {
-        var r = this.dataSeriesCodecCache.get(dataSeriesName);
+    }
+    getCodecForDataSeries(dataSeriesName) {
+        let r = this.dataSeriesCodecCache[dataSeriesName];
         if (r === undefined) {
-            var encodingData = this.dataSeriesEncoding[dataSeriesName];
+            const encodingData = this.dataSeriesEncoding[dataSeriesName];
             if (encodingData) {
-                var dataType = dataSeriesTypes[dataSeriesName];
+                const dataType = dataSeriesTypes[dataSeriesName];
                 if (!dataType) {
-                    throw new errors_1.CramMalformedError("data series name ".concat(dataSeriesName, " not defined in file compression header"));
+                    throw new errors_1.CramMalformedError(`data series name ${dataSeriesName} not defined in file compression header`);
                 }
                 r = (0, codecs_1.instantiateCodec)(encodingData, dataType);
-                this.dataSeriesCodecCache.set(dataSeriesName, r);
+                // didn't find a way to make TS understand this
+                this.dataSeriesCodecCache[dataSeriesName] = r;
             }
         }
         return r;
-    };
-    CramContainerCompressionScheme.prototype.toJSON = function () {
-        var _this = this;
-        var data = {};
-        Object.keys(this).forEach(function (k) {
+    }
+    toJSON() {
+        const data = {};
+        Object.keys(this).forEach(k => {
             if (/Cache$/.test(k)) {
                 return;
             }
-            data[k] = _this[k];
+            data[k] = this[k];
         });
         return data;
-    };
-    return CramContainerCompressionScheme;
-}());
+    }
+}
 exports.default = CramContainerCompressionScheme;
 //# sourceMappingURL=compressionScheme.js.map

package/dist/cramFile/container/compressionScheme.js.map

@@ -1 +1 @@
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+{"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.ts"],"names":[],"mappings":";;AAAA,sCAA4C;AAI5C,yCAAiD;AAMjD,sDAAsD;AACtD,aAAa;AACb,MAAM,eAAe,GAAG;IACtB,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,KAAK;IACT,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,MAAM;IACV,EAAE,EAAE,WAAW;IACf,EAAE,EAAE,KAAK;IACT,gBAAgB;IAChB,gBAAgB;CACR,CAAA;AAIV,SAAS,uBAAuB,CAAC,SAAmB;IAClD,MAAM,MAAM,GAAe,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE;QAC7B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;KACzB;IAED,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IACxC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;IAExC,OAAO,MAAM,CAAA;AACf,CAAC;AAMD,MAAqB,8BAA8B;IAcjD,YAAY,OAA8B;QARnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAOnD,+BAA+B;QAC/B,iEAAiE;QACjE,IAAI,CAAC,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAChD,IAAI,CAAC,OAAO,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QACtC,IAAI,CAAC,iBAAiB,GAAG,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAClD,IAAI,CAAC,gBAAgB,GAAG,OAAO,CAAC,YAAY,CAAC,EAAE,CAAA;QAC/C,IAAI,CAAC,kBAAkB,GAAG,uBAAuB,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC,CAAA;QAC1E,IAAI,CAAC,kBAAkB,GAAG,OAAO,CAAC,kBAAkB,CAAA;QACpD,IAAI,CAAC,WAAW,GAAG,OAAO,CAAC,WAAW,CAAA;QACtC,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;QACxC,IAAI,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,CAAA;QAC1B,IAAI,CAAC,YAAY,GAAG,OAAO,CAAC,YAAY,CAAA;IAC1C,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,YAAY,EAAE;gBAChB,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAA,yBAAgB,EAC5C,YAAY,EACZ,WAAW,CACZ,CAAA;aACF;SACF;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,SAAiB;QAC3B,OAAO,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,qBAAqB,CACnB,cAA2B;QAE3B,IAAI,CAAC,GACH,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,CAAA;QAC3C,IAAI,CAAC,KAAK,SAAS,EAAE;YACnB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE;gBAChB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,IAAI,CAAC,QAAQ,EAAE;oBACb,MAAM,IAAI,2BAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;iBACF;gBACD,CAAC,GAAG,IAAA,yBAAgB,EAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBAC5C,+CAA+C;gBAC/C,IAAI,CAAC,oBAAoB,CAAC,cAAc,CAAC,GAAG,CAAmB,CAAA;aAChE;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,MAAM;QACJ,MAAM,IAAI,GAAQ,EAAE,CAAA;QACpB,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC5B,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;gBACpB,OAAM;aACP;YACD,IAAI,CAAC,CAAC,CAAC,GAAI,IAAY,CAAC,CAAC,CAAC,CAAA;QAC5B,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CA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package/dist/cramFile/container/index.d.ts

@@ -1,13 +1,27 @@
+/// <reference types="node" />
+import CramSlice from '../slice';
+import CramContainerCompressionScheme from './compressionScheme';
+import CramFile from '../file';
 export default class CramContainer {
-    constructor(cramFile: any, position: any);
-    file: any;
-    filePosition: any;
+    file: CramFile;
+    filePosition: number;
+    constructor(file: CramFile, filePosition: number);
     getHeader(): Promise<any>;
-    getCompressionHeaderBlock(): Promise<any>;
-    getFirstBlock(): Promise<any>;
+    getCompressionHeaderBlock(): Promise<{
+        parsedContent: import("../util").ParsedItem<import("../sectionParsers").CramCompressionHeader>;
+        compressionMethod: import("../sectionParsers").CompressionMethod;
+        contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+        contentId: number;
+        compressedSize: number;
+        uncompressedSize: number;
+        _endPosition: number;
+        contentPosition: number;
+        _size: number;
+        content: Buffer;
+        crc32?: number | undefined;
+    } | null | undefined>;
+    getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
     getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
-    getSlice(slicePosition: any, sliceSize: any): CramSlice;
-    _readContainerHeader(position: any): Promise<any>;
+    getSlice(slicePosition: number, sliceSize: number): CramSlice;
+    _readContainerHeader(position: number): Promise<any>;
 }
-import CramContainerCompressionScheme from "./compressionScheme";
-import CramSlice from "../slice";

package/dist/cramFile/container/index.js

@@ -8,169 +8,99 @@ var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, ge
         step((generator = generator.apply(thisArg, _arguments || [])).next());
     });
 };
-var __generator = (this && this.__generator) || function (thisArg, body) {
-    var _ = { label: 0, sent: function() { if (t[0] & 1) throw t[1]; return t[1]; }, trys: [], ops: [] }, f, y, t, g;
-    return g = { next: verb(0), "throw": verb(1), "return": verb(2) }, typeof Symbol === "function" && (g[Symbol.iterator] = function() { return this; }), g;
-    function verb(n) { return function (v) { return step([n, v]); }; }
-    function step(op) {
-        if (f) throw new TypeError("Generator is already executing.");
-        while (_) try {
-            if (f = 1, y && (t = op[0] & 2 ? y["return"] : op[0] ? y["throw"] || ((t = y["return"]) && t.call(y), 0) : y.next) && !(t = t.call(y, op[1])).done) return t;
-            if (y = 0, t) op = [op[0] & 2, t.value];
-            switch (op[0]) {
-                case 0: case 1: t = op; break;
-                case 4: _.label++; return { value: op[1], done: false };
-                case 5: _.label++; y = op[1]; op = [0]; continue;
-                case 7: op = _.ops.pop(); _.trys.pop(); continue;
-                default:
-                    if (!(t = _.trys, t = t.length > 0 && t[t.length - 1]) && (op[0] === 6 || op[0] === 2)) { _ = 0; continue; }
-                    if (op[0] === 3 && (!t || (op[1] > t[0] && op[1] < t[3]))) { _.label = op[1]; break; }
-                    if (op[0] === 6 && _.label < t[1]) { _.label = t[1]; t = op; break; }
-                    if (t && _.label < t[2]) { _.label = t[2]; _.ops.push(op); break; }
-                    if (t[2]) _.ops.pop();
-                    _.trys.pop(); continue;
-            }
-            op = body.call(thisArg, _);
-        } catch (e) { op = [6, e]; y = 0; } finally { f = t = 0; }
-        if (op[0] & 5) throw op[1]; return { value: op[0] ? op[1] : void 0, done: true };
-    }
-};
 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 util_1 = require("../util");
-var slice_1 = __importDefault(require("../slice"));
-var compressionScheme_1 = __importDefault(require("./compressionScheme"));
-var CramContainer = /** @class */ (function () {
-    function CramContainer(cramFile, position) {
-        // cram file this container comes from
-        this.file = cramFile;
-        // position of this container in the file
-        this.filePosition = position;
-        // console.log(`container: ${this.filePosition}`)
+const errors_1 = require("../../errors");
+const util_1 = require("../util");
+const slice_1 = __importDefault(require("../slice"));
+const compressionScheme_1 = __importDefault(require("./compressionScheme"));
+class CramContainer {
+    constructor(file, filePosition) {
+        this.file = file;
+        this.filePosition = filePosition;
     }
     // memoize
-    CramContainer.prototype.getHeader = function () {
+    getHeader() {
         return this._readContainerHeader(this.filePosition);
-    };
+    }
     // memoize
-    CramContainer.prototype.getCompressionHeaderBlock = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var containerHeader, sectionParsers, block, content;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.getHeader()
-                        // if there are no records in the container, there will be no compression header
-                    ];
-                    case 1:
-                        containerHeader = _a.sent();
-                        // if there are no records in the container, there will be no compression header
-                        if (!containerHeader.numRecords) {
-                            return [2 /*return*/, null];
-                        }
-                        return [4 /*yield*/, this.file.getSectionParsers()];
-                    case 2:
-                        sectionParsers = _a.sent();
-                        return [4 /*yield*/, this.getFirstBlock()];
-                    case 3:
-                        block = _a.sent();
-                        if (block.contentType !== 'COMPRESSION_HEADER') {
-                            throw new errors_1.CramMalformedError("invalid content type ".concat(block.contentType, " in what is supposed to be the compression header block"));
-                        }
-                        content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
-                        block.content = content;
-                        return [2 /*return*/, block];
-                }
-            });
+    getCompressionHeaderBlock() {
+        return __awaiter(this, void 0, void 0, function* () {
+            const containerHeader = yield this.getHeader();
+            // if there are no records in the container, there will be no compression header
+            if (!containerHeader.numRecords) {
+                return null;
+            }
+            const sectionParsers = yield this.file.getSectionParsers();
+            const block = yield this.getFirstBlock();
+            if (block === undefined) {
+                return undefined;
+            }
+            if (block.contentType !== 'COMPRESSION_HEADER') {
+                throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in what is supposed to be the compression header block`);
+            }
+            const content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
+            return Object.assign(Object.assign({}, block), { parsedContent: content });
         });
-    };
-    CramContainer.prototype.getFirstBlock = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var containerHeader;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.getHeader()];
-                    case 1:
-                        containerHeader = _a.sent();
-                        return [2 /*return*/, this.file.readBlock(containerHeader._endPosition)];
-                }
-            });
+    }
+    getFirstBlock() {
+        return __awaiter(this, void 0, void 0, function* () {
+            const containerHeader = yield this.getHeader();
+            return this.file.readBlock(containerHeader._endPosition);
         });
-    };
+    }
     // parses the compression header data into a CramContainerCompressionScheme object
     // memoize
-    CramContainer.prototype.getCompressionScheme = function () {
-        return __awaiter(this, void 0, void 0, function () {
-            var header;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.getCompressionHeaderBlock()];
-                    case 1:
-                        header = _a.sent();
-                        if (!header) {
-                            return [2 /*return*/, undefined];
-                        }
-                        return [2 /*return*/, new compressionScheme_1.default(header.content)];
-                }
-            });
+    getCompressionScheme() {
+        return __awaiter(this, void 0, void 0, function* () {
+            const header = yield this.getCompressionHeaderBlock();
+            if (!header) {
+                return undefined;
+            }
+            return new compressionScheme_1.default(header.parsedContent);
         });
-    };
-    CramContainer.prototype.getSlice = function (slicePosition, sliceSize) {
+    }
+    getSlice(slicePosition, sliceSize) {
         // note: slicePosition is relative to the end of the container header
         // TODO: perhaps we should cache slices?
         return new slice_1.default(this, slicePosition, sliceSize);
-    };
-    CramContainer.prototype._readContainerHeader = function (position) {
-        return __awaiter(this, void 0, void 0, function () {
-            var sectionParsers, cramContainerHeader1, cramContainerHeader2, fileSize, bytes1, header1, numLandmarksSize, bytes2, header2, completeHeader;
-            return __generator(this, function (_a) {
-                switch (_a.label) {
-                    case 0: return [4 /*yield*/, this.file.getSectionParsers()];
-                    case 1:
-                        sectionParsers = _a.sent();
-                        cramContainerHeader1 = sectionParsers.cramContainerHeader1, cramContainerHeader2 = sectionParsers.cramContainerHeader2;
-                        return [4 /*yield*/, this.file.stat()];
-                    case 2:
-                        fileSize = (_a.sent()).size;
-                        if (position >= fileSize) {
-                            return [2 /*return*/, undefined];
-                        }
-                        bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
-                        return [4 /*yield*/, this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position)];
-                    case 3:
-                        _a.sent();
-                        header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
-                        numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
-                        if (position + header1.length >= fileSize) {
-                            console.warn("".concat(this.file, ": container header at ").concat(position, " indicates that the container has length ").concat(header1.length, ", which extends beyond the length of the file. Skipping this container."));
-                            return [2 /*return*/, undefined];
-                        }
-                        bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
-                        return [4 /*yield*/, this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize)];
-                    case 4:
-                        _a.sent();
-                        header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
-                        if (!(this.file.validateChecksums && header2.crc32 !== undefined)) return [3 /*break*/, 6];
-                        return [4 /*yield*/, this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, "container header beginning at position ".concat(position))];
-                    case 5:
-                        _a.sent();
-                        _a.label = 6;
-                    case 6:
-                        completeHeader = Object.assign(header1, header2, {
-                            _size: header1._size + header2._size - numLandmarksSize,
-                            _endPosition: header1._size + header2._size - numLandmarksSize + position,
-                        });
-                        return [2 /*return*/, completeHeader];
-                }
+    }
+    _readContainerHeader(position) {
+        return __awaiter(this, void 0, void 0, function* () {
+            const sectionParsers = yield this.file.getSectionParsers();
+            const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
+            const { size: fileSize } = yield this.file.stat();
+            if (position >= fileSize) {
+                return undefined;
+            }
+            // parse the container header. do it in 2 pieces because you cannot tell
+            // how much to buffer until you read numLandmarks
+            const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
+            yield this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
+            const header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
+            const numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
+            if (position + header1.length >= fileSize) {
+                console.warn(`${this.file}: container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`);
+                return undefined;
+            }
+            const bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
+            yield this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
+            const header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
+            if (this.file.validateChecksums && header2.crc32 !== undefined) {
+                yield this.file.checkCrc32(position, header1._size + header2._size - numLandmarksSize - 4, header2.crc32, `container header beginning at position ${position}`);
+            }
+            const completeHeader = Object.assign(header1, header2, {
+                _size: header1._size + header2._size - numLandmarksSize,
+                _endPosition: header1._size + header2._size - numLandmarksSize + position,
             });
+            return completeHeader;
         });
-    };
-    return CramContainer;
-}());
+    }
+}
 exports.default = CramContainer;
 'getHeader getCompressionHeaderBlock getCompressionScheme'
     .split(' ')
-    .forEach(function (method) { return (0, util_1.tinyMemoize)(CramContainer, method); });
+    .forEach(method => (0, util_1.tinyMemoize)(CramContainer, method));
 //# sourceMappingURL=index.js.map

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

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package/dist/cramFile/encoding.d.ts

@@ -0,0 +1,78 @@
+export declare type NullEncoding = {
+    codecId: 0;
+    parametersBytes: number;
+    parameters: Record<string, never>;
+};
+export declare type ExternalCramEncoding = {
+    codecId: 1;
+    parametersBytes: number;
+    parameters: {
+        blockContentId: number;
+    };
+};
+export declare type GolombEncoding = {
+    codecId: 2;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        M: number;
+    };
+};
+export declare type HuffmanEncoding = {
+    codecId: 3;
+    parametersBytes: number;
+    parameters: {
+        numCodes: number;
+        symbols: number[];
+        numLengths: number;
+        bitLengths: number[];
+    };
+};
+export declare type ByteArrayLengthEncoding = {
+    codecId: 4;
+    parametersBytes: number;
+    parameters: {
+        lengthsEncoding: CramEncoding;
+        valuesEncoding: CramEncoding;
+    };
+};
+export declare type ByteArrayStopCramEncoding = {
+    codecId: 5;
+    parametersBytes: number;
+    parameters: {
+        stopByte: number;
+        blockContentId: number;
+    };
+};
+export declare type BetaEncoding = {
+    codecId: 6;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        length: number;
+    };
+};
+export declare type SubexpEncoding = {
+    codecId: 7;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        K: number;
+    };
+};
+export declare type GolombRiceEncoding = {
+    codecId: 8;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+        log2m: number;
+    };
+};
+export declare type GammaEncoding = {
+    codecId: 9;
+    parametersBytes: number;
+    parameters: {
+        offset: number;
+    };
+};
+export declare type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;

package/dist/cramFile/encoding.js

@@ -0,0 +1,3 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=encoding.js.map