@gmod/cram 2.0.3 → 3.0.0

package/dist/cram-bundle.js.LICENSE.txt

@@ -18,6 +18,4 @@
  * @license  MIT
  */
 
-/*! https://mths.be/punycode v1.4.1 by @mathias */
-
 /*! ieee754. BSD-3-Clause License. Feross Aboukhadijeh <https://feross.org/opensource> */

package/dist/cramFile/codecs/byteArrayLength.js

@@ -3,8 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("../util");
 const _base_1 = __importDefault(require("./_base"));
+const util_1 = require("../util");
 class ByteArrayStopCodec extends _base_1.default {
     constructor(parameters, dataType, instantiateCodec) {
         super(parameters, dataType);

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,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"}
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":";;;;;AAAA,oDAA4C;AAK5C,kCAAqC;AAOrC,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.d.ts

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import CramCodec, { Cursor, Cursors } from './_base';
 import CramSlice from '../slice';
 import { CramFileBlock } from '../file';

package/dist/cramFile/codecs/external.js

@@ -25,7 +25,7 @@ class ExternalCodec extends _base_1.default {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
         if (!contentBlock) {
-            throw new errors_1.CramMalformedError(`no block found with content ID ${blockContentId}`);
+            throw new errors_1.CramMalformedError(`no block found with content ID ${blockContentId}}`);
         }
         const cursor = cursors.externalBlocks.getCursor(blockContentId);
         return this._decodeData(contentBlock, cursor);

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,sDAAsD;AACtD,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,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;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,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,CAAC;YACvD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF;AA3DD,gCA2DC"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,sDAAsD;AACtD,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,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,cAAc,GAAG,CACpD,CAAA;QACH,CAAC;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,CAAC;YACvD,MAAM,IAAI,gCAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF;AA3DD,gCA2DC"}

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

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 export declare class CramBufferOverrunError extends Error {
 }
 export declare function getBits(data: Buffer, cursor: {

package/dist/cramFile/codecs/getBits.js

@@ -1,6 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.getBits = exports.CramBufferOverrunError = void 0;
+exports.CramBufferOverrunError = void 0;
+exports.getBits = getBits;
 class CramBufferOverrunError extends Error {
 }
 exports.CramBufferOverrunError = CramBufferOverrunError;
@@ -22,5 +23,4 @@ function getBits(data, cursor, numBits) {
     }
     return val;
 }
-exports.getBits = getBits;
 //# sourceMappingURL=getBits.js.map

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

@@ -1 +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,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"}
+{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAEA,0BAyBC;AA3BD,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"}

package/dist/cramFile/codecs/huffman.js

@@ -28,7 +28,8 @@ class HuffmanIntCodec extends _base_1.default {
         this.buildCodeBook();
         this.buildCodes();
         this.buildCaches();
-        // if this is a degenerate zero-length huffman code, special-case the decoding
+        // if this is a degenerate zero-length huffman code, special-case the
+        // decoding
         if (this.sortedCodes[0].bitLength === 0) {
             this._decode = this._decodeZeroLengthCode;
         }

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,sDAAsD;AACtD,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;AAQD,MAAqB,eAAgB,SAAQ,eAG5C;IASC,YACE,UAAyC,EACzC,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAZrB,UAAK,GAAyB,EAAE,CAAA;QAChC,aAAQ,GAA6B,EAAE,CAAA;QACvC,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,CAAC;YAC7C,MAAM,IAAI,SAAS,CACjB,GAAG,IAAI,CAAC,QAAQ,oDAAoD,CACrE,CAAA;QACH,CAAC;QAED,IAAI,CAAC,aAAa,EAAE,CAAA;QACpB,IAAI,CAAC,UAAU,EAAE,CAAA;QACjB,IAAI,CAAC,WAAW,EAAE,CAAA;QAElB,qEAAqE;QACrE,WAAW;QACX,IAAI,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,KAAK,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,qBAAqB,CAAA;QAC3C,CAAC;IACH,CAAC;IAED,aAAa;QACX,8DAA8D;QAC9D,IAAI,KAAK,GAAG,IAAI,KAAK,CACnB,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,CAAC;YACrD,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;QACH,CAAC;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,CAAC;gBACnC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,CAAA;YACpC,CAAC;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,CAAC;oBAC9C,MAAM,IAAI,2BAAkB,CAAC,qBAAqB,CAAC,CAAA;gBACrD,CAAC;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,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,CAAC;YACvD,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACtD,CAAC;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,CAAC;YACpD,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,CAAC;gBACC,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,CAAC;oBACnE,OAAO,IAAI,CAAC,qBAAqB,CAAC,KAAK,CAAC,CAAA;gBAC1C,CAAC;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,MAAM,EAC3B,CAAC,IAAI,CAAC,EACN,CAAC;oBACD,CAAC,IAAI,CAAC,CAAA;gBACR,CAAC;YACH,CAAC;QACH,CAAC;QACD,MA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package/dist/cramFile/codecs/index.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.instantiateCodec = void 0;
+exports.instantiateCodec = instantiateCodec;
 const errors_1 = require("../../errors");
 const huffman_1 = __importDefault(require("./huffman"));
 const external_1 = __importDefault(require("./external"));
@@ -33,5 +33,4 @@ function instantiateCodec(encodingData, dataType) {
     }
     return new CodecClass(encodingData.parameters, dataType, instantiateCodec);
 }
-exports.instantiateCodec = instantiateCodec;
 //# sourceMappingURL=index.js.map

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

@@ -1 +1 @@
-{"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"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/index.ts"],"names":[],"mappings":";;;;;AA6BA,4CAcC;AA3CD,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"}

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

@@ -48,9 +48,6 @@ export default class CramContainerCompressionScheme {
     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

package/dist/cramFile/container/compressionScheme.js

@@ -70,7 +70,6 @@ class CramContainerCompressionScheme {
         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;
@@ -79,9 +78,6 @@ class CramContainerCompressionScheme {
         this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
         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

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,CAAC;QAC9B,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IAC1B,CAAC;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;IAWjD,YAAY,OAA8B;QALnC,yBAAoB,GAAoB,EAAE,CAAA;QAC1C,kBAAa,GAA8B,EAAE,CAAA;QAC7C,gBAAW,GAAiC,EAAE,CAAA;QAInD,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;IACxC,CAAC;IAED;;;OAGG;IACH,cAAc,CAAC,OAAe;QAC5B,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE,CAAC;YACjC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,YAAY,EAAE,CAAC;gBACjB,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,IAAA,yBAAgB,EAC5C,YAAY,EACZ,WAAW,CACZ,CAAA;YACH,CAAC;QACH,CAAC;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,CAAC;YACpB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE,CAAC;gBACjB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,IAAI,CAAC,QAAQ,EAAE,CAAC;oBACd,MAAM,IAAI,2BAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;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;YACjE,CAAC;QACH,CAAC;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,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,EAAE,CAAC;gBACxB,OAAM;YACR,CAAC;YACD,IAAI,CAAC,CAAC,CAAC,GAAI,IAAY,CAAC,CAAC,CAAC,CAAA;QAC5B,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF;AAhFD,iDAgFC"}

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

@@ -1,4 +1,3 @@
-/// <reference types="node" />
 import CramSlice from '../slice';
 import CramContainerCompressionScheme from './compressionScheme';
 import CramFile from '../file';
@@ -6,9 +5,39 @@ export default class CramContainer {
     file: CramFile;
     filePosition: number;
     constructor(file: CramFile, filePosition: number);
-    getHeader(): Promise<any>;
+    getHeader(): Promise<({
+        length: number;
+        refSeqId: number;
+        refSeqStart: number;
+        alignmentSpan: number;
+        numBlocks: number;
+        numLandmarks: number;
+        numBases: number | undefined;
+        recordCounter: number;
+        numRecords: number;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        _size: number;
+        _endPosition: number;
+    }) | undefined>;
     getCompressionHeaderBlock(): Promise<{
-        parsedContent: import("../util").ParsedItem<import("../sectionParsers").CramCompressionHeader>;
+        parsedContent: {
+            dataSeriesEncoding: import("../codecs/dataSeriesTypes").DataSeriesEncodingMap;
+            preservation: import("../sectionParsers").CramPreservationMap;
+            tagEncoding: Record<string, import("../encoding").CramEncoding>;
+        } & {
+            _endPosition: number;
+            _size: number;
+        };
         compressionMethod: import("../sectionParsers").CompressionMethod;
         contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
         contentId: number;
@@ -18,10 +47,33 @@ export default class CramContainer {
         contentPosition: number;
         _size: number;
         content: Buffer;
-        crc32?: number | undefined;
+        crc32?: number;
     } | null | undefined>;
     getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
     getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
     getSlice(slicePosition: number, sliceSize: number): CramSlice;
-    _readContainerHeader(position: number): Promise<any>;
+    _readContainerHeader(position: number): Promise<({
+        length: number;
+        refSeqId: number;
+        refSeqStart: number;
+        alignmentSpan: number;
+        numBlocks: number;
+        numLandmarks: number;
+        numBases: number | undefined;
+        recordCounter: number;
+        numRecords: number;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        _size: number;
+        _endPosition: number;
+    }) | undefined>;
 }

package/dist/cramFile/container/index.js

@@ -16,24 +16,25 @@ const errors_1 = require("../../errors");
 const util_1 = require("../util");
 const slice_1 = __importDefault(require("../slice"));
 const compressionScheme_1 = __importDefault(require("./compressionScheme"));
+const sectionParsers_1 = require("../sectionParsers");
 class CramContainer {
     constructor(file, filePosition) {
         this.file = file;
         this.filePosition = filePosition;
     }
-    // memoize
     getHeader() {
         return this._readContainerHeader(this.filePosition);
     }
-    // memoize
     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) {
+            // if there are no records in the container, there will be no compression
+            // header
+            if (!(containerHeader === null || containerHeader === void 0 ? void 0 : containerHeader.numRecords)) {
                 return null;
             }
-            const sectionParsers = yield this.file.getSectionParsers();
+            const { majorVersion } = yield this.file.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const block = yield this.getFirstBlock();
             if (block === undefined) {
                 return undefined;
@@ -48,11 +49,14 @@ class CramContainer {
     getFirstBlock() {
         return __awaiter(this, void 0, void 0, function* () {
             const containerHeader = yield this.getHeader();
+            if (!containerHeader) {
+                return undefined;
+            }
             return this.file.readBlock(containerHeader._endPosition);
         });
     }
-    // parses the compression header data into a CramContainerCompressionScheme object
-    // memoize
+    // parses the compression header data into a CramContainerCompressionScheme
+    // object
     getCompressionScheme() {
         return __awaiter(this, void 0, void 0, function* () {
             const header = yield this.getCompressionHeaderBlock();
@@ -69,10 +73,12 @@ class CramContainer {
     }
     _readContainerHeader(position) {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.file.getSectionParsers();
+            const { majorVersion } = yield this.file.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
             const { size: fileSize } = yield this.file.stat();
             if (position >= fileSize) {
+                console.warn(`position:${position}>=fileSize:${fileSize} in cram container`);
                 return undefined;
             }
             // parse the container header. do it in 2 pieces because you cannot tell
@@ -82,7 +88,7 @@ class CramContainer {
             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.`);
+                console.warn(`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));

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

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,yCAAiD;AAEjD,kCAA0D;AAC1D,qDAAgC;AAChC,4EAAgE;AAEhE,sDAAqD;AAErD,MAAqB,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAEK,yBAAyB;;YAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAE9C,yEAAyE;YACzE,SAAS;YACT,IAAI,CAAC,CAAA,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,UAAU,CAAA,EAAE,CAAC;gBACjC,OAAO,IAAI,CAAA;YACb,CAAC;YACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;YACxD,MAAM,cAAc,GAAG,IAAA,kCAAiB,EAAC,YAAY,CAAC,CAAA;YAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;YACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;gBAC/C,MAAM,IAAI,2BAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,yDAAyD,CACnG,CAAA;YACH,CAAC;YAED,MAAM,OAAO,GAAG,IAAA,gBAAS,EACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;YACD,uCACK,KAAK,KACR,aAAa,EAAE,OAAO,IACvB;QACH,CAAC;KAAA;IAEK,aAAa;;YACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,IAAI,CAAC,eAAe,EAAE,CAAC;gBACrB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;QAC1D,CAAC;KAAA;IAED,2EAA2E;IAC3E,SAAS;IACH,oBAAoB;;YACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;YACrD,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,OAAO,SAAS,CAAA;YAClB,CAAC;YAED,OAAO,IAAI,2BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;QACjE,CAAC;KAAA;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,eAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAEK,oBAAoB,CAAC,QAAgB;;YACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;YACxD,MAAM,cAAc,GAAG,IAAA,kCAAiB,EAAC,YAAY,CAAC,CAAA;YACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;YACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;gBACzB,OAAO,CAAC,IAAI,CACV,YAAY,QAAQ,cAAc,QAAQ,oBAAoB,CAC/D,CAAA;gBACD,OAAO,SAAS,CAAA;YAClB,CAAC;YAED,wEAAwE;YACxE,iDAAiD;YACjD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;YACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;YACzE,MAAM,OAAO,GAAG,IAAA,gBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;YAC9D,MAAM,gBAAgB,GAAG,IAAA,eAAQ,EAAC,OAAO,CAAC,YAAY,CAAC,CAAA;YACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;gBAC1C,OAAO,CAAC,IAAI,CACV,uBAAuB,QAAQ,4CAA4C,OAAO,CAAC,MAAM,yEAAyE,CACnK,CAAA;gBACD,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;YACD,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAClB,MAAM,EACN,CAAC,EACD,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;YACD,MAAM,OAAO,GAAG,IAAA,gBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;YAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;gBAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;YACH,CAAC;YAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;gBACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;gBACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;aAC1E,CAAC,CAAA;YAEF,OAAO,cAAc,CAAA;QACvB,CAAC;KAAA;CACF;AAxHD,gCAwHC;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}

package/dist/cramFile/file.d.ts

@@ -1,7 +1,4 @@
-/// <reference path="../../src/typings/binary-parser.d.ts" />
-/// <reference types="node" />
 import QuickLRU from 'quick-lru';
-import { Parser } from '@gmod/binary-parser';
 import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
 import CramRecord from './record';
@@ -40,7 +37,12 @@ export default class CramFile {
         buffer: Buffer;
     }>;
     stat(): Promise<import("generic-filehandle").Stats>;
-    getDefinition(): Promise<any>;
+    getDefinition(): Promise<{
+        magic: string;
+        majorVersion: number;
+        minorVersion: number;
+        fileId: string;
+    }>;
     getSamHeader(): Promise<{
         tag: string;
         data: {
@@ -49,60 +51,6 @@ export default class CramFile {
         }[];
     }[]>;
     getHeaderText(): Promise<string | undefined>;
-    getSectionParsers(): Promise<{
-        cramFileDefinition: {
-            parser: Parser<{
-                magic: string;
-                majorVersion: number;
-                minorVersion: number;
-                fileId: string;
-            }>;
-            maxLength: number;
-        };
-        cramContainerHeader1: {
-            parser: Parser<{
-                length: number;
-                refSeqId: number;
-                refSeqStart: number;
-                alignmentSpan: number;
-                numRecords: number;
-                recordCounter: number;
-                numBases: number;
-                numBlocks: number;
-                numLandmarks: number;
-            }>;
-            maxLength: number;
-        };
-        cramContainerHeader2: {
-            parser: Parser<{
-                numLandmarks: number;
-                landmarks: number[];
-                crc32: number;
-            }>;
-            maxLength: (x: number) => number;
-        };
-        cramBlockHeader: {
-            parser: Parser<BlockHeader>;
-            maxLength: number;
-        };
-        cramBlockCrc32: {
-            parser: Parser<{
-                crc32: number;
-            }>;
-            maxLength: number;
-        };
-        cramCompressionHeader: {
-            parser: Parser<import("./sectionParsers").CramCompressionHeader>;
-        };
-        cramMappedSliceHeader: {
-            parser: Parser<import("./sectionParsers").MappedSliceHeader>;
-            maxLength: (numContentIds: number) => number;
-        };
-        cramUnmappedSliceHeader: {
-            parser: Parser<import("./sectionParsers").UnmappedSliceHeader>;
-            maxLength: (numContentIds: number) => number;
-        };
-    }>;
     getContainerById(containerNumber: number): Promise<CramContainer | undefined>;
     checkCrc32(position: number, length: number, recordedCrc32: number, description: string): Promise<void>;
     /**
@@ -110,11 +58,26 @@ export default class CramFile {
      */
     containerCount(): Promise<number | undefined>;
     getContainerAtPosition(position: number): CramContainer;
-    readBlockHeader(position: number): Promise<import("./util").ParsedItem<BlockHeader> | undefined>;
+    readBlockHeader(position: number): Promise<({
+        uncompressedSize: number;
+        compressedSize: number;
+        contentId: number;
+        contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+        compressionMethod: CompressionMethod;
+    } & {
+        _endPosition: number;
+        _size: number;
+    }) | undefined>;
     _parseSection<T>(section: {
-        parser: Parser<T>;
         maxLength: number;
-    }, position: number, size?: number, preReadBuffer?: undefined): Promise<import("./util").ParsedItem<T> | undefined>;
+        parser: (buffer: Buffer, offset: number) => {
+            offset: number;
+            value: T;
+        };
+    }, position: number, size?: number, preReadBuffer?: undefined): Promise<(T & {
+        _endPosition: number;
+        _size: number;
+    }) | undefined>;
     _uncompress(compressionMethod: CompressionMethod, inputBuffer: Buffer, outputBuffer: Buffer): Promise<void>;
     readBlock(position: number): Promise<CramFileBlock | undefined>;
 }

package/dist/cramFile/file.js

@@ -34,18 +34,18 @@ function bufferToStream(buf) {
         },
     });
 }
-//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+// source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
     const uInt32 = new Uint32Array([0x11223344]);
     const uInt8 = new Uint8Array(uInt32.buffer);
     if (uInt8[0] === 0x44) {
-        return 0; //little-endian
+        return 0; // little-endian
     }
     else if (uInt8[0] === 0x11) {
-        return 1; //big-endian
+        return 1; // big-endian
     }
     else {
-        return 2; //mixed-endian?
+        return 2; // mixed-endian?
     }
 }
 class CramFile {
@@ -80,10 +80,10 @@ class CramFile {
     // memoized
     getDefinition() {
         return __awaiter(this, void 0, void 0, function* () {
-            const headbytes = Buffer.allocUnsafe(sectionParsers_1.cramFileDefinition.maxLength);
-            yield this.file.read(headbytes, 0, sectionParsers_1.cramFileDefinition.maxLength, 0);
-            const definition = sectionParsers_1.cramFileDefinition.parser.parse(headbytes)
-                .result;
+            const { maxLength, parser } = (0, sectionParsers_1.cramFileDefinition)();
+            const headbytes = Buffer.allocUnsafe(maxLength);
+            yield this.file.read(headbytes, 0, maxLength, 0);
+            const definition = parser(headbytes).value;
             if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
                 throw new errors_1.CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
             }
@@ -119,22 +119,16 @@ class CramFile {
             return this.header;
         });
     }
-    // memoize
-    getSectionParsers() {
-        return __awaiter(this, void 0, void 0, function* () {
-            const { majorVersion } = yield this.getDefinition();
-            return (0, sectionParsers_1.getSectionParsers)(majorVersion);
-        });
-    }
     getContainerById(containerNumber) {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.getSectionParsers();
+            const { majorVersion } = yield this.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             let position = sectionParsers.cramFileDefinition.maxLength;
             const { size: fileSize } = yield this.file.stat();
             const { cramContainerHeader1 } = sectionParsers;
             // skip with a series of reads to the proper container
             let currentContainer;
-            for (let i = 0; i <= containerNumber; i += 1) {
+            for (let i = 0; i <= containerNumber; i++) {
                 // if we are about to go off the end of the file
                 // and have not found that container, it does not exist
                 if (position + cramContainerHeader1.maxLength + 8 >= fileSize) {
@@ -145,13 +139,12 @@ class CramFile {
                 if (!currentHeader) {
                     throw new errors_1.CramMalformedError(`container ${containerNumber} not found in file`);
                 }
-                // if this is the first container, read all the blocks in the
-                // container to determine its length, because we cannot trust
-                // the container header's given length due to a bug somewhere
-                // in htslib
+                // if this is the first container, read all the blocks in the container
+                // to determine its length, because we cannot trust the container
+                // header's given length due to a bug somewhere in htslib
                 if (i === 0) {
                     position = currentHeader._endPosition;
-                    for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+                    for (let j = 0; j < currentHeader.numBlocks; j++) {
                         const block = yield this.readBlock(position);
                         if (block === undefined) {
                             return undefined;
@@ -182,7 +175,8 @@ class CramFile {
      */
     containerCount() {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.getSectionParsers();
+            const { majorVersion } = yield this.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const { size: fileSize } = yield this.file.stat();
             const { cramContainerHeader1 } = sectionParsers;
             let containerCount = 0;
@@ -197,7 +191,7 @@ class CramFile {
                 // header's given length due to a bug somewhere in htslib
                 if (containerCount === 0) {
                     position = currentHeader._endPosition;
-                    for (let j = 0; j < currentHeader.numBlocks; j += 1) {
+                    for (let j = 0; j < currentHeader.numBlocks; j++) {
                         const block = yield this.readBlock(position);
                         if (block === undefined) {
                             return undefined;
@@ -219,7 +213,8 @@ class CramFile {
     }
     readBlockHeader(position) {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.getSectionParsers();
+            const { majorVersion } = yield this.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const { cramBlockHeader } = sectionParsers;
             const { size: fileSize } = yield this.file.stat();
             if (position + cramBlockHeader.maxLength >= fileSize) {
@@ -230,8 +225,8 @@ class CramFile {
             return (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
         });
     }
-    _parseSection(section, position, size = section.maxLength, preReadBuffer = undefined) {
-        return __awaiter(this, void 0, void 0, function* () {
+    _parseSection(section_1, position_1) {
+        return __awaiter(this, arguments, void 0, function* (section, position, size = section.maxLength, preReadBuffer = undefined) {
             let buffer;
             if (preReadBuffer) {
                 buffer = preReadBuffer;
@@ -301,7 +296,7 @@ class CramFile {
     readBlock(position) {
         return __awaiter(this, void 0, void 0, function* () {
             const { majorVersion } = yield this.getDefinition();
-            const sectionParsers = yield this.getSectionParsers();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const blockHeader = yield this.readBlockHeader(position);
             if (blockHeader === undefined) {
                 return undefined;