@gmod/cram 2.0.0 → 2.0.2

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

@@ -1,24 +1,24 @@
 import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
 import { DataType } from './dataSeriesTypes';
-export type DataTypeMapping = {
+export interface DataTypeMapping {
     byte: number;
     int: number;
     long: number;
     byteArray: Uint8Array;
-};
-export type Cursor = {
+}
+export interface Cursor {
     bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
     bytePosition: number;
-};
-export type Cursors = {
+}
+export interface Cursors {
     lastAlignmentStart: number;
     coreBlock: Cursor;
     externalBlocks: {
         map: Map<any, any>;
         getCursor: (contentId: number) => Cursor;
     };
-};
+}
 export default abstract class CramCodec<TResult extends DataType = DataType, TParameters = unknown> {
     parameters: TParameters;
     dataType: DataType;

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

@@ -1 +1 @@
-{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,SAAU,SAAQ,eAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;SACF;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF;AA1BD,4BA0BC"}
+{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,SAAU,SAAQ,eAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,IAAA,iBAAO,EACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF;AA1BD,4BA0BC"}

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

@@ -1 +1 @@
-{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,kCAAqC;AAErC,oDAA4C;AAW5C,MAAqB,kBAAmB,SAAQ,eAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,MAAM,IAAI,SAAS,CACjB,8CAA8C,QAAQ,EAAE,CACzD,CAAA;SACF;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,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;YACvC,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,MAAM,CACxB,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;SACF;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;AA3DD,qCA2DC;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAC,CAAA"}
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,kCAAqC;AAErC,oDAA4C;AAW5C,MAAqB,kBAAmB,SAAQ,eAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE,CAAC;YAC7B,MAAM,IAAI,SAAS,CACjB,8CAA8C,QAAQ,EAAE,CACzD,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,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,GAAG,SAAS,CAAC,MAAM,CACxB,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QACH,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;AA3DD,qCA2DC;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,CAAC,CAAA"}

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

@@ -1 +1 @@
-{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":";;;;;AAAA,yCAAiD;AAEjD,oDAAoD;AAIpD,uCAAkD;AAElD,MAAqB,kBAAmB,SAAQ,eAG/C;IACC,YACE,UAAmD,EACnD,QAAqB;QAErB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,MAAM,IAAI,SAAS,CACjB,kDAAkD,QAAQ,EAAE,CAC7D,CAAA;SACF;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;QACtD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;SACF;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,gBAAgB,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,gBAAgB,CAAC,YAA2B,EAAE,MAAc;QAC1D,MAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QACvC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,6BAA6B;QAC7B,MAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAA;QACzC,IAAI,YAAY,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,OACE,UAAU,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrC,YAAY,GAAG,UAAU,CAAC,MAAM,EAChC;YACA,IAAI,YAAY,KAAK,UAAU,CAAC,MAAM,EAAE;gBACtC,MAAM,IAAI,gCAAsB,CAC9B,qDAAqD,CACtD,CAAA;aACF;YACD,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;SAChC;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACzD,CAAC;CACF;AArDD,qCAqDC"}
+{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":";;;;;AAAA,yCAAiD;AAEjD,oDAAoD;AAIpD,uCAAkD;AAElD,MAAqB,kBAAmB,SAAQ,eAG/C;IACC,YACE,UAAmD,EACnD,QAAqB;QAErB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,QAAQ,KAAK,WAAW,EAAE,CAAC;YAC7B,MAAM,IAAI,SAAS,CACjB,kDAAkD,QAAQ,EAAE,CAC7D,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;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,gBAAgB,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,gBAAgB,CAAC,YAA2B,EAAE,MAAc;QAC1D,MAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QACvC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,6BAA6B;QAC7B,MAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAA;QACzC,IAAI,YAAY,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,OACE,UAAU,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrC,YAAY,GAAG,UAAU,CAAC,MAAM,EAChC,CAAC;YACD,IAAI,YAAY,KAAK,UAAU,CAAC,MAAM,EAAE,CAAC;gBACvC,MAAM,IAAI,gCAAsB,CAC9B,qDAAqD,CACtD,CAAA;YACH,CAAC;YACD,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACjC,CAAC;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACzD,CAAC;CACF;AArDD,qCAqDC"}

package/dist/cramFile/codecs/external.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/unbound-method */
 const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const util_1 = require("../util");

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,yCAAyE;AACzE,oDAAoD;AACpD,kCAAmC;AAGnC,uCAAkD;AAGlD,MAAqB,aAAc,SAAQ,eAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;SACnC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE;YACnC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;SACpC;aAAM;YACL,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;SACF;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;QACtD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;SACF;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,IAAA,gBAAS,EACnC,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;YACtD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;SACF;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF;AA3DD,gCA2DC"}
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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,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;QACH,CAAC;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,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;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.js.map

@@ -1 +1 @@
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+{"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,CAAC;QACD,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;IACH,CAAC;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;QACtC,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,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QAC1B,CAAC;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAzBD,0BAyBC"}

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

@@ -5,7 +5,6 @@ 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;

package/dist/cramFile/codecs/huffman.js

@@ -3,6 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+/* eslint-disable @typescript-eslint/unbound-method */
 const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const getBits_1 = require("./getBits");
@@ -16,7 +17,6 @@ class HuffmanIntCodec extends _base_1.default {
         super(parameters, dataType);
         this.codes = {};
         this.codeBook = {};
-        this.sortedByValue = [];
         this.sortedCodes = [];
         this.sortedValuesByBitCode = [];
         this.sortedBitCodes = [];
@@ -78,8 +78,6 @@ class HuffmanIntCodec extends _base_1.default {
     }
     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((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);

package/dist/cramFile/codecs/huffman.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,CAAC;QAChB,MAAM,IAAI,+BAAsB,CAC9B,qCAAqC,YAAY,CAAC,OAAO,EAAE,CAC5D,CAAA;IACH,CAAC;IAED,OAAO,IAAI,UAAU,CAAC,YAAY,CAAC,UAAU,EAAE,QAAQ,EAAE,gBAAgB,CAAC,CAAA;AAC5E,CAAC;AAdD,4CAcC"}

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,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;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,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAC,CAAA;QACL,IAAI,CAAC,CAAA;QACL,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,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;QAC1D,CAAC;aAAM,CAAC;YACN,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;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF;AArCD,8BAqCC"}

package/dist/cramFile/container/compressionScheme.js

@@ -123,7 +123,7 @@ class CramContainerCompressionScheme {
     toJSON() {
         const data = {};
         Object.keys(this).forEach(k => {
-            if (/Cache$/.test(k)) {
+            if (k.endsWith('Cache')) {
                 return;
             }
             data[k] = this[k];

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

@@ -1 +1 @@
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package/dist/cramFile/container/index.js.map

@@ -1 +1 @@
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package/dist/cramFile/encoding.d.ts

@@ -1,24 +1,24 @@
-export type NullEncoding = {
+export interface NullEncoding {
     codecId: 0;
     parametersBytes: number;
     parameters: Record<string, never>;
-};
-export type ExternalCramEncoding = {
+}
+export interface ExternalCramEncoding {
     codecId: 1;
     parametersBytes: number;
     parameters: {
         blockContentId: number;
     };
-};
-export type GolombEncoding = {
+}
+export interface GolombEncoding {
     codecId: 2;
     parametersBytes: number;
     parameters: {
         offset: number;
         M: number;
     };
-};
-export type HuffmanEncoding = {
+}
+export interface HuffmanEncoding {
     codecId: 3;
     parametersBytes: number;
     parameters: {
@@ -27,52 +27,52 @@ export type HuffmanEncoding = {
         numLengths: number;
         bitLengths: number[];
     };
-};
-export type ByteArrayLengthEncoding = {
+}
+export interface ByteArrayLengthEncoding {
     codecId: 4;
     parametersBytes: number;
     parameters: {
         lengthsEncoding: CramEncoding;
         valuesEncoding: CramEncoding;
     };
-};
-export type ByteArrayStopCramEncoding = {
+}
+export interface ByteArrayStopCramEncoding {
     codecId: 5;
     parametersBytes: number;
     parameters: {
         stopByte: number;
         blockContentId: number;
     };
-};
-export type BetaEncoding = {
+}
+export interface BetaEncoding {
     codecId: 6;
     parametersBytes: number;
     parameters: {
         offset: number;
         length: number;
     };
-};
-export type SubexpEncoding = {
+}
+export interface SubexpEncoding {
     codecId: 7;
     parametersBytes: number;
     parameters: {
         offset: number;
         K: number;
     };
-};
-export type GolombRiceEncoding = {
+}
+export interface GolombRiceEncoding {
     codecId: 8;
     parametersBytes: number;
     parameters: {
         offset: number;
         log2m: number;
     };
-};
-export type GammaEncoding = {
+}
+export interface GammaEncoding {
     codecId: 9;
     parametersBytes: number;
     parameters: {
         offset: number;
     };
-};
+}
 export type CramEncoding = NullEncoding | ExternalCramEncoding | GolombEncoding | HuffmanEncoding | ByteArrayLengthEncoding | ByteArrayStopCramEncoding | BetaEncoding | SubexpEncoding | GolombRiceEncoding | GammaEncoding;

package/dist/cramFile/file.d.ts

@@ -1,3 +1,4 @@
+/// <reference path="../../src/typings/binary-parser.d.ts" />
 /// <reference types="node" />
 import QuickLRU from 'quick-lru';
 import { Parser } from '@gmod/binary-parser';
@@ -5,16 +6,16 @@ import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
 import CramRecord from './record';
 import { Filehandle } from './filehandle';
-export type CramFileSource = {
+export interface CramFileSource {
     filehandle?: Filehandle;
     url?: string;
     path?: string;
-};
+}
 export type SeqFetch = (seqId: number, start: number, end: number) => Promise<string>;
 export type CramFileArgs = CramFileSource & {
-    checkSequenceMD5: boolean;
+    checkSequenceMD5?: boolean;
     cacheSize?: number;
-    seqFetch: SeqFetch;
+    seqFetch?: SeqFetch;
 };
 export type CramFileBlock = BlockHeader & {
     _endPosition: number;
@@ -26,9 +27,9 @@ export type CramFileBlock = BlockHeader & {
 export default class CramFile {
     private file;
     validateChecksums: boolean;
-    fetchReferenceSequenceCallback: SeqFetch;
+    fetchReferenceSequenceCallback?: SeqFetch;
     options: {
-        checkSequenceMD5: boolean;
+        checkSequenceMD5?: boolean;
         cacheSize: number;
     };
     featureCache: QuickLRU<string, Promise<CramRecord[]>>;
@@ -40,7 +41,13 @@ export default class CramFile {
     }>;
     stat(): Promise<import("generic-filehandle").Stats>;
     getDefinition(): Promise<any>;
-    getSamHeader(): Promise<import("../sam").HeaderDataItem[]>;
+    getSamHeader(): Promise<{
+        tag: string;
+        data: {
+            tag: string;
+            value: string | undefined;
+        }[];
+    }[]>;
     getHeaderText(): Promise<string | undefined>;
     getSectionParsers(): Promise<{
         cramFileDefinition: {

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/filehandle.d.ts

@@ -1,2 +1 @@
-import { GenericFilehandle } from 'generic-filehandle';
-export { GenericFilehandle as Filehandle };
+export { GenericFilehandle as Filehandle } from 'generic-filehandle';

package/dist/cramFile/index.d.ts

@@ -1,3 +1,2 @@
-import CramFile from './file';
 export { default as CramRecord } from './record';
-export default CramFile;
+export { default } from './file';

package/dist/cramFile/index.js

@@ -3,9 +3,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.CramRecord = void 0;
-const file_1 = __importDefault(require("./file"));
+exports.default = exports.CramRecord = void 0;
 var record_1 = require("./record");
 Object.defineProperty(exports, "CramRecord", { enumerable: true, get: function () { return __importDefault(record_1).default; } });
-exports.default = file_1.default;
+var file_1 = require("./file");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(file_1).default; } });
 //# sourceMappingURL=index.js.map

package/dist/cramFile/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":";;;;;;AAAA,kDAA6B;AAC7B,mCAAgD;AAAvC,qHAAA,OAAO,OAAc;AAE9B,kBAAe,cAAQ,CAAA"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cramFile/index.ts"],"names":[],"mappings":";;;;;;AAAA,mCAAgD;AAAvC,qHAAA,OAAO,OAAc;AAE9B,+BAAgC;AAAvB,gHAAA,OAAO,OAAA"}

package/dist/cramFile/record.d.ts

@@ -1,25 +1,25 @@
 import CramContainerCompressionScheme from './container/compressionScheme';
 import decodeRecord from './slice/decodeRecord';
-export type RefRegion = {
+export interface RefRegion {
     start: number;
     end: number;
     seq: string;
-};
-export type ReadFeature = {
+}
+export interface ReadFeature {
     code: string;
     pos: number;
     refPos: number;
     data: any;
     ref?: string;
     sub?: string;
-};
-export type MateRecord = {
+}
+export interface MateRecord {
     readName?: string;
     sequenceId: number;
     alignmentStart: number;
     flags?: number;
     uniqueId?: number;
-};
+}
 export declare const BamFlags: readonly [readonly [1, "Paired"], readonly [2, "ProperlyPaired"], readonly [4, "SegmentUnmapped"], readonly [8, "MateUnmapped"], readonly [16, "ReverseComplemented"], readonly [32, "MateReverseComplemented"], readonly [64, "Read1"], readonly [128, "Read2"], readonly [256, "Secondary"], readonly [512, "FailedQc"], readonly [1024, "Duplicate"], readonly [2048, "Supplementary"]];
 export declare const CramFlags: readonly [readonly [1, "PreservingQualityScores"], readonly [2, "Detached"], readonly [4, "WithMateDownstream"], readonly [8, "DecodeSequenceAsStar"]];
 export declare const MateFlags: readonly [readonly [1, "OnNegativeStrand"], readonly [2, "Unmapped"]];

package/dist/cramFile/record.js

@@ -17,7 +17,7 @@ function decodeReadSequence(cramRecord, refRegion) {
     const regionSeqOffset = cramRecord.alignmentStart - refRegion.start;
     if (!cramRecord.readFeatures) {
         return refRegion.seq
-            .substr(regionSeqOffset, cramRecord.lengthOnRef)
+            .slice(regionSeqOffset, regionSeqOffset + (cramRecord.lengthOnRef || 0))
             .toUpperCase();
     }
     let bases = '';
@@ -81,14 +81,17 @@ function decodeReadSequence(cramRecord, refRegion) {
             }
             else if (currentReadFeature < cramRecord.readFeatures.length) {
                 // put down a chunk of sequence up to the next read feature
-                const chunk = refRegion.seq.substr(regionPos, cramRecord.readFeatures[currentReadFeature].pos - bases.length - 1);
+                const chunk = refRegion.seq.slice(regionPos, regionPos +
+                    cramRecord.readFeatures[currentReadFeature].pos -
+                    bases.length -
+                    1);
                 bases += chunk;
                 regionPos += chunk.length;
             }
         }
         else {
             // put down a chunk of reference up to the full read length
-            const chunk = refRegion.seq.substr(regionPos, cramRecord.readLength - bases.length);
+            const chunk = refRegion.seq.slice(regionPos, regionPos + cramRecord.readLength - bases.length);
             bases += chunk;
             regionPos += chunk.length;
         }
@@ -368,7 +371,7 @@ class CramRecord {
     toJSON() {
         const data = {};
         Object.keys(this).forEach(k => {
-            if (k.charAt(0) === '_') {
+            if (k.startsWith('_')) {
                 return;
             }
             data[k] = this[k];

package/dist/cramFile/record.js.map

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