@gmod/cram 1.6.2 → 1.6.3

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

@@ -1,7 +1,7 @@
 export default class ByteArrayStopCodec extends CramCodec {
     constructor(parameters: {} | undefined, dataType: any, instantiateCodec: any);
     instantiateCodec: any;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any[];
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): Uint8Array;
     _getLengthCodec(): any;
     _getDataCodec(): any;
 }

package/dist/cramFile/codecs/byteArrayLength.js

@@ -35,7 +35,7 @@ var ByteArrayStopCodec = /** @class */ (function (_super) {
         var lengthCodec = this._getLengthCodec();
         var arrayLength = lengthCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
         var dataCodec = this._getDataCodec();
-        var data = new Array(arrayLength);
+        var data = new Uint8Array(arrayLength);
         for (var i = 0; i < arrayLength; i += 1) {
             data[i] = dataCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
         }

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

@@ -1 +1 @@
-{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,gCAAqC;AAErC,kDAA+B;AAE/B;IAAgD,sCAAS;IACvD,4BAAY,UAAe,EAAE,QAAQ,EAAE,gBAAgB;QAA3C,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAO5B;QANC,KAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,MAAM,IAAI,SAAS,CACjB,qDAA8C,QAAQ,CAAE,CACzD,CAAA;SACF;;IACH,CAAC;IAED,mCAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,IAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,IAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,IAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,IAAM,IAAI,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;QACnC,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,4CAAe,GAAf;QACE,IAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,0CAAa,GAAb;QACE,IAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QAErD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;IACH,yBAAC;AAAD,CAAC,AA9CD,CAAgD,eAAS,GA8CxD;;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,UAAA,MAAM,IAAI,OAAA,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,EAAvC,CAAuC,CAAC,CAAA"}
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,gCAAqC;AAErC,kDAA+B;AAE/B;IAAgD,sCAAS;IACvD,4BAAY,UAAe,EAAE,QAAQ,EAAE,gBAAgB;QAA3C,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAO5B;QANC,KAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,MAAM,IAAI,SAAS,CACjB,qDAA8C,QAAQ,CAAE,CACzD,CAAA;SACF;;IACH,CAAC;IAED,mCAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,IAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,IAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,IAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,IAAM,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,4CAAe,GAAf;QACE,IAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,0CAAa,GAAb;QACE,IAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QAErD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;IACH,yBAAC;AAAD,CAAC,AA9CD,CAAgD,eAAS,GA8CxD;;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,UAAA,MAAM,IAAI,OAAA,IAAA,kBAAW,EAAC,kBAAkB,EAAE,MAAM,CAAC,EAAvC,CAAuC,CAAC,CAAA"}

package/dist/cramFile/codecs/byteArrayStop.js

@@ -56,8 +56,7 @@ var ByteArrayStopCodec = /** @class */ (function (_super) {
             stopPosition += 1;
         }
         cursor.bytePosition = stopPosition + 1;
-        var data = dataBuffer.slice(startPosition, stopPosition);
-        return data;
+        return dataBuffer.slice(startPosition, stopPosition);
     };
     return ByteArrayStopCodec;
 }(_base_1.default));

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

@@ -1 +1 @@
-{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,uCAAyE;AAEzE,kDAA+B;AAE/B;IAAgD,sCAAS;IACvD,4BAAY,UAAe,EAAE,QAAQ;QAAzB,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAQ5B;QAPC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,KAAI,CAAC,OAAO,GAAG,KAAI,CAAC,gBAAgB,CAAA;SACrC;aAAM;YACL,MAAM,IAAI,SAAS,CACjB,yDAAkD,QAAQ,CAAE,CAC7D,CAAA;SACF;;IACH,CAAC;IAED,mCAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QAC7C,IAAA,cAAc,GAAK,IAAI,CAAC,UAAU,eAApB,CAAoB;QAC1C,IAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,2BAAkB,CAC1B,yCAAkC,cAAc,CAAE,CACnD,CAAA;SACF;QACD,IAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,OAAO,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC3C,CAAC;IAED,6CAAgB,GAAhB,UAAiB,YAAY,EAAE,MAAM;QACnC,IAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QAC/B,IAAA,QAAQ,GAAK,IAAI,CAAC,UAAU,SAApB,CAAoB;QACpC,6BAA6B;QAC7B,IAAM,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,+BAAsB,CAC9B,qDAAqD,CACtD,CAAA;aACF;YACD,YAAY,IAAI,CAAC,CAAA;SAClB;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,IAAM,IAAI,GAAG,UAAU,CAAC,KAAK,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;QAC1D,OAAO,IAAI,CAAA;IACb,CAAC;IACH,yBAAC;AAAD,CAAC,AA7CD,CAAgD,eAAS,GA6CxD"}
+{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,uCAAyE;AAEzE,kDAA+B;AAE/B;IAAgD,sCAAS;IACvD,4BAAY,UAAe,EAAE,QAAQ;QAAzB,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAQ5B;QAPC,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,KAAI,CAAC,OAAO,GAAG,KAAI,CAAC,gBAAgB,CAAA;SACrC;aAAM;YACL,MAAM,IAAI,SAAS,CACjB,yDAAkD,QAAQ,CAAE,CAC7D,CAAA;SACF;;IACH,CAAC;IAED,mCAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QAC7C,IAAA,cAAc,GAAK,IAAI,CAAC,UAAU,eAApB,CAAoB;QAC1C,IAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,2BAAkB,CAC1B,yCAAkC,cAAc,CAAE,CACnD,CAAA;SACF;QACD,IAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,OAAO,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC3C,CAAC;IAED,6CAAgB,GAAhB,UAAiB,YAAY,EAAE,MAAM;QACnC,IAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QAC/B,IAAA,QAAQ,GAAK,IAAI,CAAC,UAAU,SAApB,CAAoB;QACpC,6BAA6B;QAC7B,IAAM,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,+BAAsB,CAC9B,qDAAqD,CACtD,CAAA;aACF;YACD,YAAY,IAAI,CAAC,CAAA;SAClB;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,KAAK,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACtD,CAAC;IACH,yBAAC;AAAD,CAAC,AA5CD,CAAgD,eAAS,GA4CxD"}

package/dist/cramFile/codecs/external.js

@@ -55,9 +55,7 @@ var ExternalCodec = /** @class */ (function (_super) {
         if (cursor.bytePosition >= contentBlock.content.length) {
             throw new errors_1.CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
         }
-        var result = contentBlock.content[cursor.bytePosition];
-        cursor.bytePosition += 1;
-        return result;
+        return contentBlock.content[cursor.bytePosition++];
     };
     return ExternalCodec;
 }(_base_1.default));

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,uCAIqB;AACrB,kDAA+B;AAC/B,gCAAmC;AAEnC;IAA2C,iCAAS;IAClD,uBAAY,UAAe,EAAE,QAAQ;QAAzB,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAU5B;QATC,IAAI,KAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,KAAI,CAAC,WAAW,GAAG,KAAI,CAAC,UAAU,CAAA;SACnC;aAAM,IAAI,KAAI,CAAC,QAAQ,KAAK,MAAM,EAAE;YACnC,KAAI,CAAC,WAAW,GAAG,KAAI,CAAC,WAAW,CAAA;SACpC;aAAM;YACL,MAAM,IAAI,+BAAsB,CAC9B,UAAG,KAAI,CAAC,QAAQ,oDAAiD,CAClE,CAAA;SACF;;IACH,CAAC;IAED,8BAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QAC7C,IAAA,cAAc,GAAK,IAAI,CAAC,UAAU,eAApB,CAAoB;QAC1C,IAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,2BAAkB,CAC1B,yCAAkC,cAAc,CAAE,CACnD,CAAA;SACF;QACD,IAAM,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,kCAAU,GAAV,UAAW,YAAY,EAAE,MAAM;QACvB,IAAA,KAAsB,IAAA,gBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,EAHM,MAAM,QAAA,EAAE,SAAS,QAGvB,CAAA;QACD,MAAM,CAAC,YAAY,IAAI,SAAS,CAAA;QAChC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,mCAAW,GAAX,UAAY,YAAY,EAAE,MAAM;QAC9B,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE;YACtD,MAAM,IAAI,+BAAsB,CAC9B,mEAAmE,CACpE,CAAA;SACF;QACD,IAAM,MAAM,GAAG,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,CAAC,CAAA;QACxD,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;IACH,oBAAC;AAAD,CAAC,AA7CD,CAA2C,eAAS,GA6CnD"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;AAAA,uCAIqB;AACrB,kDAA+B;AAC/B,gCAAmC;AAEnC;IAA2C,iCAAS;IAClD,uBAAY,UAAe,EAAE,QAAQ;QAAzB,2BAAA,EAAA,eAAe;QAA3B,YACE,kBAAM,UAAU,EAAE,QAAQ,CAAC,SAU5B;QATC,IAAI,KAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,KAAI,CAAC,WAAW,GAAG,KAAI,CAAC,UAAU,CAAA;SACnC;aAAM,IAAI,KAAI,CAAC,QAAQ,KAAK,MAAM,EAAE;YACnC,KAAI,CAAC,WAAW,GAAG,KAAI,CAAC,WAAW,CAAA;SACpC;aAAM;YACL,MAAM,IAAI,+BAAsB,CAC9B,UAAG,KAAI,CAAC,QAAQ,oDAAiD,CAClE,CAAA;SACF;;IACH,CAAC;IAED,8BAAM,GAAN,UAAO,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QAC7C,IAAA,cAAc,GAAK,IAAI,CAAC,UAAU,eAApB,CAAoB;QAC1C,IAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE;YACjB,MAAM,IAAI,2BAAkB,CAC1B,yCAAkC,cAAc,CAAE,CACnD,CAAA;SACF;QACD,IAAM,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,kCAAU,GAAV,UAAW,YAAY,EAAE,MAAM;QACvB,IAAA,KAAsB,IAAA,gBAAS,EACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,EAHM,MAAM,QAAA,EAAE,SAAS,QAGvB,CAAA;QACD,MAAM,CAAC,YAAY,IAAI,SAAS,CAAA;QAChC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,mCAAW,GAAX,UAAY,YAAY,EAAE,MAAM;QAC9B,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE;YACtD,MAAM,IAAI,+BAAsB,CAC9B,mEAAmE,CACpE,CAAA;SACF;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;IACH,oBAAC;AAAD,CAAC,AA3CD,CAA2C,eAAS,GA2CnD"}

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

@@ -5,7 +5,7 @@ export default class CramContainerCompressionScheme {
     referenceRequired: boolean;
     tagIdsDictionary: any;
     substitutionMatrix: any[];
-    dataSeriesCodecCache: {};
+    dataSeriesCodecCache: Map<any, any>;
     tagCodecCache: {};
     /**
      * @param {string} tagName three-character tag name

package/dist/cramFile/container/compressionScheme.js

@@ -74,7 +74,7 @@ var CramContainerCompressionScheme = /** @class */ (function () {
         this.referenceRequired = !!content.preservation.RR;
         this.tagIdsDictionary = content.preservation.TD;
         this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
-        this.dataSeriesCodecCache = {};
+        this.dataSeriesCodecCache = new Map();
         this.tagCodecCache = {};
     }
     /**
@@ -99,17 +99,19 @@ var CramContainerCompressionScheme = /** @class */ (function () {
         return this.tagIdsDictionary[tagListId];
     };
     CramContainerCompressionScheme.prototype.getCodecForDataSeries = function (dataSeriesName) {
-        if (!this.dataSeriesCodecCache[dataSeriesName]) {
+        var r = this.dataSeriesCodecCache.get(dataSeriesName);
+        if (r === undefined) {
             var encodingData = this.dataSeriesEncoding[dataSeriesName];
             if (encodingData) {
                 var dataType = dataSeriesTypes[dataSeriesName];
                 if (!dataType) {
                     throw new errors_1.CramMalformedError("data series name ".concat(dataSeriesName, " not defined in file compression header"));
                 }
-                this.dataSeriesCodecCache[dataSeriesName] = (0, codecs_1.instantiateCodec)(encodingData, dataType);
+                r = (0, codecs_1.instantiateCodec)(encodingData, dataType);
+                this.dataSeriesCodecCache.set(dataSeriesName, r);
             }
         }
-        return this.dataSeriesCodecCache[dataSeriesName];
+        return r;
     };
     CramContainerCompressionScheme.prototype.toJSON = function () {
         var _this = this;

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

@@ -1 +1 @@
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+{"version":3,"file":"compressionScheme.js","sourceRoot":"","sources":["../../../src/cramFile/container/compressionScheme.js"],"names":[],"mappings":";;AAAA,uCAAiD;AACjD,oCAA4C;AAE5C,sDAAsD;AACtD,aAAa;AACb,IAAM,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,EAAE,EAAE,QAAQ;IACZ,EAAE,EAAE,QAAQ;CACb,CAAA;AAED,SAAS,uBAAuB,CAAC,SAAS;IACxC,IAAM,MAAM,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IAC3B,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;AAED;IACE,wCAAY,OAAO;QACjB,MAAM,CAAC,MAAM,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QAC5B,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;QAE1E,IAAI,CAAC,oBAAoB,GAAG,IAAI,GAAG,EAAE,CAAA;QACrC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAA;IACzB,CAAC;IAED;;;OAGG;IACH,uDAAc,GAAd,UAAe,OAAO;QACpB,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,IAAM,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,oDAAW,GAAX,UAAY,SAAS;QACnB,OAAO,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,8DAAqB,GAArB,UAAsB,cAAc;QAClC,IAAI,CAAC,GAAG,IAAI,CAAC,oBAAoB,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;QACrD,IAAI,CAAC,KAAK,SAAS,EAAE;YACnB,IAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE;gBAChB,IAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,IAAI,CAAC,QAAQ,EAAE;oBACb,MAAM,IAAI,2BAAkB,CAC1B,2BAAoB,cAAc,4CAAyC,CAC5E,CAAA;iBACF;gBACD,CAAC,GAAG,IAAA,yBAAgB,EAAC,YAAY,EAAE,QAAQ,CAAC,CAAA;gBAC5C,IAAI,CAAC,oBAAoB,CAAC,GAAG,CAAC,cAAc,EAAE,CAAC,CAAC,CAAA;aACjD;SACF;QACD,OAAO,CAAC,CAAA;IACV,CAAC;IAED,+CAAM,GAAN;QAAA,iBASC;QARC,IAAM,IAAI,GAAG,EAAE,CAAA;QACf,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,UAAA,CAAC;YACzB,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;gBACpB,OAAM;aACP;YACD,IAAI,CAAC,CAAC,CAAC,GAAG,KAAI,CAAC,CAAC,CAAC,CAAA;QACnB,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;IACH,qCAAC;AAAD,CAAC,AApED,IAoEC"}

package/dist/cramFile/file.js

@@ -50,6 +50,20 @@ var container_1 = __importDefault(require("./container"));
 var io_1 = require("../io");
 var util_1 = require("./util");
 var sam_1 = require("../sam");
+//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+function getEndianness() {
+    var uInt32 = new Uint32Array([0x11223344]);
+    var uInt8 = new Uint8Array(uInt32.buffer);
+    if (uInt8[0] === 0x44) {
+        return 0; //little-endian
+    }
+    else if (uInt8[0] === 0x11) {
+        return 1; //big-endian
+    }
+    else {
+        return 2; //mixed-endian?
+    }
+}
 var CramFile = /** @class */ (function () {
     /**
      * @param {object} args
@@ -78,6 +92,9 @@ var CramFile = /** @class */ (function () {
         this.featureCache = new quick_lru_1.default({
             maxSize: this.options.cacheSize,
         });
+        if (getEndianness() > 0) {
+            throw new Error('Detected big-endian machine, may be unable to run');
+        }
     }
     CramFile.prototype.toString = function () {
         if (this.file.filename) {

package/dist/cramFile/file.js.map

@@ -1 +1 @@
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package/dist/cramFile/slice/decodeRecord.js

@@ -11,12 +11,12 @@ var constants_1 = __importDefault(require("../constants"));
  * given a Buffer, read a string up to the first null character
  * @private
  */
-function readNullTerminatedStringFromBuffer(buffer) {
-    var zeroOffset = buffer.indexOf(0);
-    if (zeroOffset === -1) {
-        return buffer.toString('utf8');
+function readNullTerminatedString(buffer) {
+    var r = '';
+    for (var i = 0; i < buffer.length && buffer[i] !== 0; i++) {
+        r += String.fromCharCode(buffer[i]);
     }
-    return buffer.toString('utf8', 0, zeroOffset);
+    return r;
 }
 /**
  * parse a BAM tag's array value from a binary buffer
@@ -24,67 +24,86 @@ function readNullTerminatedStringFromBuffer(buffer) {
  */
 function parseTagValueArray(buffer) {
     var arrayType = String.fromCharCode(buffer[0]);
-    var length = buffer.readInt32LE(1);
-    var schema = {
-        c: ['readInt8', 1],
-        C: ['readUInt8', 1],
-        s: ['readInt16LE', 2],
-        S: ['readUInt16LE', 2],
-        i: ['readInt32LE', 4],
-        I: ['readUInt32LE', 4],
-        f: ['readFloatLE', 4],
-    }[arrayType];
-    if (!schema) {
-        throw new errors_1.CramMalformedError("invalid tag value array type '".concat(arrayType, "'"));
-    }
-    var getMethod = schema[0], itemSize = schema[1];
+    var length = Int32Array.from(buffer.slice(1))[0];
     var array = new Array(length);
-    var offset = 5;
-    for (var i = 0; i < length; i += 1) {
-        array[i] = buffer[getMethod](offset);
-        offset += itemSize;
+    buffer = buffer.slice(5);
+    if (arrayType === 'c') {
+        var arr = new Int8Array(buffer.buffer);
+        for (var i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'C') {
+        var arr = new Uint8Array(buffer.buffer);
+        for (var i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 's') {
+        var arr = new Int16Array(buffer.buffer);
+        for (var i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'S') {
+        var arr = new Uint16Array(buffer.buffer);
+        for (var i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'i') {
+        var arr = new Int32Array(buffer.buffer);
+        for (var i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'I') {
+        var arr = new Uint32Array(buffer.buffer);
+        for (var i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'f') {
+        var arr = new Float32Array(buffer.buffer);
+        for (var i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else {
+        throw new Error('unknown type: ' + arrayType);
     }
     return array;
 }
 function parseTagData(tagType, buffer) {
-    if (!buffer.readInt32LE) {
-        buffer = Buffer.from(buffer);
-    }
     if (tagType === 'Z') {
-        return readNullTerminatedStringFromBuffer(buffer);
+        return readNullTerminatedString(buffer);
     }
     if (tagType === 'A') {
         return String.fromCharCode(buffer[0]);
     }
     if (tagType === 'I') {
-        var val = long_1.default.fromBytesLE(buffer);
-        if (val.greaterThan(Number.MAX_SAFE_INTEGER) ||
-            val.lessThan(Number.MIN_SAFE_INTEGER)) {
-            throw new errors_1.CramUnimplementedError('integer overflow');
-        }
-        return val.toNumber();
+        return long_1.default.fromBytesLE(buffer).toNumber();
     }
     if (tagType === 'i') {
-        return buffer.readInt32LE(0);
+        return new Int32Array(buffer.buffer)[0];
     }
     if (tagType === 's') {
-        return buffer.readInt16LE(0);
+        return new Int16Array(buffer.buffer)[0];
     }
     if (tagType === 'S') {
-        return buffer.readUInt16LE(0);
+        return new Uint16Array(buffer.buffer)[0];
     }
     if (tagType === 'c') {
-        return buffer.readInt8(0);
+        return new Int8Array(buffer.buffer)[0];
     }
     if (tagType === 'C') {
-        return buffer.readUInt8(0);
+        return buffer[0];
     }
     if (tagType === 'f') {
-        return buffer.readFloatLE(0);
+        return new Float32Array(buffer.buffer)[0];
     }
     if (tagType === 'H') {
-        var hex = readNullTerminatedStringFromBuffer(buffer);
-        return Number.parseInt(hex.replace(/^0x/, ''), 16);
+        return Number.parseInt(readNullTerminatedString(buffer).replace(/^0x/, ''), 16);
     }
     if (tagType === 'B') {
         return parseTagValueArray(buffer);
@@ -158,21 +177,6 @@ function decodeReadFeatures(cramRecord, readFeatureCount, decodeDataSeries, comp
     }
     return readFeatures;
 }
-function thingToString(thing) {
-    if (thing instanceof Buffer) {
-        return readNullTerminatedStringFromBuffer(thing);
-    }
-    if (thing.length && thing.indexOf) {
-        // array-like
-        if (!thing[thing.length - 1]) {
-            // trim zeroes off the end if necessary
-            var termIndex = thing.indexOf(0);
-            return String.fromCharCode.apply(String, thing.slice(0, termIndex));
-        }
-        return String.fromCharCode.apply(String, thing);
-    }
-    return String(thing);
-}
 function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
     var cramRecord = new record_1.default();
     cramRecord.flags = decodeDataSeries('BF');
@@ -195,7 +199,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     cursors.lastAlignmentStart = cramRecord.alignmentStart;
     cramRecord.readGroupId = decodeDataSeries('RG');
     if (compressionScheme.readNamesIncluded) {
-        cramRecord.readName = thingToString(decodeDataSeries('RN'));
+        cramRecord.readName = readNullTerminatedString(decodeDataSeries('RN'));
     }
     // mate record
     if (cramRecord.isDetached()) {
@@ -203,7 +207,7 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         var mate = {};
         mate.flags = decodeDataSeries('MF');
         if (!compressionScheme.readNamesIncluded) {
-            mate.readName = thingToString(decodeDataSeries('RN'));
+            mate.readName = readNullTerminatedString(decodeDataSeries('RN'));
             cramRecord.readName = mate.readName;
         }
         mate.sequenceId = decodeDataSeries('NS');

package/dist/cramFile/slice/decodeRecord.js.map

@@ -1 +1 @@
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package/dist/cramFile/slice/index.js

@@ -379,11 +379,14 @@ var CramSlice = /** @class */ (function () {
                             lastAlignmentStart: sliceHeader.content.refSeqStart || 0,
                             coreBlock: { bitPosition: 7, bytePosition: 0 },
                             externalBlocks: {
+                                map: new Map(),
                                 getCursor: function (contentId) {
-                                    if (!this[contentId]) {
-                                        this[contentId] = { bitPosition: 7, bytePosition: 0 };
+                                    var r = this.map.get(contentId);
+                                    if (r === undefined) {
+                                        r = { bitPosition: 7, bytePosition: 0 };
+                                        this.map.set(contentId, r);
                                     }
-                                    return this[contentId];
+                                    return r;
                                 },
                             },
                         };
@@ -416,8 +419,8 @@ var CramSlice = /** @class */ (function () {
                                 }
                             }
                         }
-                        // interpret `recordsToNextFragment` attributes to make standard `mate` objects
-                        // Resolve mate pair cross-references between records in this slice
+                        // interpret `recordsToNextFragment` attributes to make standard `mate`
+                        // objects Resolve mate pair cross-references between records in this slice
                         for (i = 0; i < records.length; i += 1) {
                             mateRecordNumber = records[i].mateRecordNumber;
                             if (mateRecordNumber >= 0) {

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

@@ -1 +1 @@
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package/esm/cramFile/codecs/byteArrayLength.d.ts

@@ -1,7 +1,7 @@
 export default class ByteArrayStopCodec extends CramCodec {
     constructor(parameters: {} | undefined, dataType: any, instantiateCodec: any);
     instantiateCodec: any;
-    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): any[];
+    decode(slice: any, coreDataBlock: any, blocksByContentId: any, cursors: any): Uint8Array;
     _getLengthCodec(): any;
     _getDataCodec(): any;
 }

package/esm/cramFile/codecs/byteArrayLength.js

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

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

@@ -1 +1 @@
-{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAErC,OAAO,SAAS,MAAM,SAAS,CAAA;AAE/B,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAAS;IACvD,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ,EAAE,gBAAgB;QACrD,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,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,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,KAAK,CAAC,WAAW,CAAC,CAAA;QACnC,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;QAErD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAC,CAAA"}
+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAErC,OAAO,SAAS,MAAM,SAAS,CAAA;AAE/B,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAAS;IACvD,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ,EAAE,gBAAgB;QACrD,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,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,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;QAErD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAC,CAAA"}

package/esm/cramFile/codecs/byteArrayStop.js

@@ -33,8 +33,7 @@ export default class ByteArrayStopCodec extends CramCodec {
             stopPosition += 1;
         }
         cursor.bytePosition = stopPosition + 1;
-        const data = dataBuffer.slice(startPosition, stopPosition);
-        return data;
+        return dataBuffer.slice(startPosition, stopPosition);
     }
 }
 //# sourceMappingURL=byteArrayStop.js.map

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

@@ -1 +1 @@
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+{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.js"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAEzE,OAAO,SAAS,MAAM,SAAS,CAAA;AAE/B,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAAS;IACvD,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ;QACnC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,QAAQ,KAAK,WAAW,EAAE;YAC5B,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,gBAAgB,CAAA;SACrC;aAAM;YACL,MAAM,IAAI,SAAS,CACjB,kDAAkD,QAAQ,EAAE,CAC7D,CAAA;SACF;IACH,CAAC;IAED,MAAM,CAAC,KAAK,EAAE,aAAa,EAAE,iBAAiB,EAAE,OAAO;QACrD,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,kBAAkB,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,OAAO,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC3C,CAAC;IAED,gBAAgB,CAAC,YAAY,EAAE,MAAM;QACnC,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,sBAAsB,CAC9B,qDAAqD,CACtD,CAAA;aACF;YACD,YAAY,IAAI,CAAC,CAAA;SAClB;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,KAAK,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACtD,CAAC;CACF"}

package/esm/cramFile/codecs/external.js

@@ -32,9 +32,7 @@ export default class ExternalCodec extends CramCodec {
         if (cursor.bytePosition >= contentBlock.content.length) {
             throw new CramBufferOverrunError('attempted to read beyond end of block. this file seems truncated.');
         }
-        const result = contentBlock.content[cursor.bytePosition];
-        cursor.bytePosition += 1;
-        return result;
+        return contentBlock.content[cursor.bytePosition++];
     }
 }
 //# sourceMappingURL=external.js.map