@gmod/cram 2.0.4 → 3.0.1

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.js

@@ -31,7 +31,7 @@ class ByteArrayStopCodec extends _base_1.default {
         while (dataBuffer[stopPosition] !== stopByte &&
             stopPosition < dataBuffer.length) {
             if (stopPosition === dataBuffer.length) {
-                throw new getBits_1.CramBufferOverrunError(`byteArrayStop reading beyond length of data buffer?`);
+                throw new getBits_1.CramBufferOverrunError('byteArrayStop reading beyond length of data buffer?');
             }
             stopPosition = stopPosition + 1;
         }

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/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;
         }
@@ -57,7 +58,7 @@ class HuffmanIntCodec extends _base_1.default {
         let codeLength = 0;
         let codeValue = -1;
         Object.entries(this.codeBook).forEach(([bitLength, symbols]) => {
-            const bitLengthInt = parseInt(bitLength, 10);
+            const bitLengthInt = Number.parseInt(bitLength, 10);
             symbols.forEach(symbol => {
                 const code = {
                     bitLength: bitLengthInt,

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

@@ -1 +1 @@
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@@ -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,CAAS,CAAA;QACb,IAAI,CAAS,CAAA;QACb,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.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

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer';
 import CramSlice from '../slice';
 import CramContainerCompressionScheme from './compressionScheme';
 import CramFile from '../file';
@@ -5,9 +6,39 @@ 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;
@@ -22,5 +53,28 @@ export default class CramContainer {
     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

@@ -12,34 +12,37 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const buffer_1 = require("buffer");
 const errors_1 = require("../../errors");
+// locals
 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;
             }
             if (block.contentType !== 'COMPRESSION_HEADER') {
-                throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in what is supposed to be the compression header block`);
+                throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
             }
             const content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
             return Object.assign(Object.assign({}, block), { parsedContent: content });
@@ -48,11 +51,14 @@ class CramContainer {
     getFirstBlock() {
         return __awaiter(this, void 0, void 0, function* () {
             const containerHeader = yield this.getHeader();
+            if (!containerHeader) {
+                return undefined;
+            }
             return this.file.readBlock(containerHeader._endPosition);
         });
     }
-    // parses the compression header data into a CramContainerCompressionScheme object
-    // memoize
+    // parses the compression header data into a CramContainerCompressionScheme
+    // object
     getCompressionScheme() {
         return __awaiter(this, void 0, void 0, function* () {
             const header = yield this.getCompressionHeaderBlock();
@@ -69,23 +75,26 @@ class CramContainer {
     }
     _readContainerHeader(position) {
         return __awaiter(this, void 0, void 0, function* () {
-            const sectionParsers = yield this.file.getSectionParsers();
+            const { majorVersion } = yield this.file.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
             const { size: fileSize } = yield this.file.stat();
             if (position >= fileSize) {
+                console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`);
                 return undefined;
             }
             // parse the container header. do it in 2 pieces because you cannot tell
             // how much to buffer until you read numLandmarks
-            const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
+            const bytes1 = buffer_1.Buffer.allocUnsafe(cramContainerHeader1.maxLength);
             yield this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
             const header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
             const numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
             if (position + header1.length >= fileSize) {
-                console.warn(`${this.file}: container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`);
+                // header indicates container goes beyond fileSize
+                console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
                 return undefined;
             }
-            const bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
+            const bytes2 = buffer_1.Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
             yield this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
             const header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
             if (this.file.validateChecksums && header2.crc32 !== undefined) {

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,mCAA+B;AAC/B,yCAAiD;AACjD,SAAS;AACT,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,8BAA8B,CACxE,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,CAAC,OAAO,QAAQ,cAAc,QAAQ,oBAAoB,CAAC,CAAA;gBACvE,OAAO,SAAS,CAAA;YAClB,CAAC;YAED,wEAAwE;YACxE,iDAAiD;YACjD,MAAM,MAAM,GAAG,eAAM,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,kDAAkD;gBAClD,OAAO,CAAC,IAAI,CACV,gBAAgB,QAAQ,uBAAuB,QAAQ,YAAY,CACpE,CAAA;gBACD,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,MAAM,GAAG,eAAM,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;AAvHD,gCAuHC;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

@@ -1,5 +1,5 @@
+import { Buffer } from 'buffer';
 import QuickLRU from 'quick-lru';
-import { Parser } from '@gmod/binary-parser';
 import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';
 import CramRecord from './record';
@@ -38,7 +38,12 @@ 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: {
@@ -47,60 +52,6 @@ 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>;
     /**
@@ -108,11 +59,26 @@ 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>;
 }