@gmod/cram 2.0.4 → 3.0.1

package/dist/rans/index.js.map

@@ -1 +1 @@
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package/esm/cramFile/codecs/byteArrayLength.js

@@ -1,5 +1,5 @@
-import { tinyMemoize } from '../util';
 import CramCodec from './_base';
+import { tinyMemoize } from '../util';
 export default class ByteArrayStopCodec extends CramCodec {
     constructor(parameters, dataType, instantiateCodec) {
         super(parameters, dataType);

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

@@ -1 +1 @@
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+{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAK5C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAOrC,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/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;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

@@ -26,7 +26,7 @@ export default class ByteArrayStopCodec extends CramCodec {
         while (dataBuffer[stopPosition] !== stopByte &&
             stopPosition < dataBuffer.length) {
             if (stopPosition === dataBuffer.length) {
-                throw new CramBufferOverrunError(`byteArrayStop reading beyond length of data buffer?`);
+                throw new CramBufferOverrunError('byteArrayStop reading beyond length of data buffer?');
             }
             stopPosition = stopPosition + 1;
         }

package/esm/cramFile/codecs/external.js

@@ -20,7 +20,7 @@ export default class ExternalCodec extends CramCodec {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
         if (!contentBlock) {
-            throw new CramMalformedError(`no block found with content ID ${blockContentId}`);
+            throw new CramMalformedError(`no block found with content ID ${blockContentId}}`);
         }
         const cursor = cursors.externalBlocks.getCursor(blockContentId);
         return this._decodeData(contentBlock, cursor);

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,sDAAsD;AACtD,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACzE,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAGnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;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,sBAAsB,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,kBAAkB,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,SAAS,CACnC,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,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,sDAAsD;AACtD,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACzE,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAGnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;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,sBAAsB,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,kBAAkB,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,SAAS,CACnC,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,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF"}

package/esm/cramFile/codecs/huffman.js

@@ -23,7 +23,8 @@ export default class HuffmanIntCodec extends CramCodec {
         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;
         }
@@ -52,7 +53,7 @@ export default class HuffmanIntCodec extends CramCodec {
         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/esm/cramFile/codecs/huffman.js.map

@@ -1 +1 @@
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package/esm/cramFile/codecs/subexp.js.map

@@ -1 +1 @@
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+{"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,WAAY,SAAQ,SAGxC;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,sBAAsB,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,OAAO,CAAC,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,OAAO,CAAC,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,OAAO,CAAC,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"}

package/esm/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/esm/cramFile/container/compressionScheme.js

@@ -68,7 +68,6 @@ export default 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;
@@ -77,9 +76,6 @@ export default 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/esm/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,OAAO,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAI5C,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;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,MAAM,CAAC,OAAO,OAAO,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,gBAAgB,CAC5C,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,kBAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;gBACH,CAAC;gBACD,CAAC,GAAG,gBAAgB,CAAC,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"}

package/esm/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/esm/cramFile/container/index.js

@@ -1,30 +1,33 @@
+import { Buffer } from 'buffer';
 import { CramMalformedError } from '../../errors';
+// locals
 import { itf8Size, parseItem, tinyMemoize } from '../util';
 import CramSlice from '../slice';
 import CramContainerCompressionScheme from './compressionScheme';
+import { getSectionParsers } from '../sectionParsers';
 export default class CramContainer {
     constructor(file, filePosition) {
         this.file = file;
         this.filePosition = filePosition;
     }
-    // memoize
     getHeader() {
         return this._readContainerHeader(this.filePosition);
     }
-    // memoize
     async getCompressionHeaderBlock() {
         const containerHeader = await 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 = await this.file.getSectionParsers();
+        const { majorVersion } = await this.file.getDefinition();
+        const sectionParsers = getSectionParsers(majorVersion);
         const block = await this.getFirstBlock();
         if (block === undefined) {
             return undefined;
         }
         if (block.contentType !== 'COMPRESSION_HEADER') {
-            throw new CramMalformedError(`invalid content type ${block.contentType} in what is supposed to be the compression header block`);
+            throw new CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
         }
         const content = parseItem(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
         return {
@@ -34,10 +37,13 @@ export default class CramContainer {
     }
     async getFirstBlock() {
         const containerHeader = await this.getHeader();
+        if (!containerHeader) {
+            return undefined;
+        }
         return this.file.readBlock(containerHeader._endPosition);
     }
-    // parses the compression header data into a CramContainerCompressionScheme object
-    // memoize
+    // parses the compression header data into a CramContainerCompressionScheme
+    // object
     async getCompressionScheme() {
         const header = await this.getCompressionHeaderBlock();
         if (!header) {
@@ -51,10 +57,12 @@ export default class CramContainer {
         return new CramSlice(this, slicePosition, sliceSize);
     }
     async _readContainerHeader(position) {
-        const sectionParsers = await this.file.getSectionParsers();
+        const { majorVersion } = await this.file.getDefinition();
+        const sectionParsers = getSectionParsers(majorVersion);
         const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
         const { size: fileSize } = await this.file.stat();
         if (position >= fileSize) {
+            console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`);
             return undefined;
         }
         // parse the container header. do it in 2 pieces because you cannot tell
@@ -64,7 +72,8 @@ export default class CramContainer {
         const header1 = parseItem(bytes1, cramContainerHeader1.parser);
         const numLandmarksSize = itf8Size(header1.numLandmarks);
         if (position + header1.length >= fileSize) {
-            console.warn(`${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));

package/esm/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,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAA;AAC/B,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,SAAS;AACT,OAAO,EAAE,QAAQ,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAC1D,OAAO,SAAS,MAAM,UAAU,CAAA;AAChC,OAAO,8BAA8B,MAAM,qBAAqB,CAAA;AAEhE,OAAO,EAAE,iBAAiB,EAAE,MAAM,mBAAmB,CAAA;AAErD,MAAM,CAAC,OAAO,OAAO,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;IAED,KAAK,CAAC,yBAAyB;QAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAE9C,yEAAyE;QACzE,SAAS;QACT,IAAI,CAAC,CAAA,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,UAAU,CAAA,EAAE,CAAC;YACjC,OAAO,IAAI,CAAA;QACb,CAAC;QACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;YAC/C,MAAM,IAAI,kBAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;QACH,CAAC;QAED,MAAM,OAAO,GAAG,SAAS,CACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;QACD,OAAO;YACL,GAAG,KAAK;YACR,aAAa,EAAE,OAAO;SACvB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;QAC9C,IAAI,CAAC,eAAe,EAAE,CAAC;YACrB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,SAAS;IACT,KAAK,CAAC,oBAAoB;QACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;QACrD,IAAI,CAAC,MAAM,EAAE,CAAC;YACZ,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,OAAO,IAAI,8BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;IACjE,CAAC;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,SAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,oBAAoB,CAAC,QAAgB;QACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;QACxD,MAAM,cAAc,GAAG,iBAAiB,CAAC,YAAY,CAAC,CAAA;QACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;YACzB,OAAO,CAAC,IAAI,CAAC,OAAO,QAAQ,cAAc,QAAQ,oBAAoB,CAAC,CAAA;YACvE,OAAO,SAAS,CAAA;QAClB,CAAC;QAED,wEAAwE;QACxE,iDAAiD;QACjD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;QACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACzE,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAC9D,MAAM,gBAAgB,GAAG,QAAQ,CAAC,OAAO,CAAC,YAAY,CAAC,CAAA;QACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;YAC1C,kDAAkD;YAClD,OAAO,CAAC,IAAI,CACV,gBAAgB,QAAQ,uBAAuB,QAAQ,YAAY,CACpE,CAAA;YACD,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;QACD,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;QACD,MAAM,OAAO,GAAG,SAAS,CAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;QAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;YAC/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;QACH,CAAC;QAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;YACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;YACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;SAC1E,CAAC,CAAA;QAEF,OAAO,cAAc,CAAA;IACvB,CAAC;CACF;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}

package/esm/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>;
 }

package/esm/cramFile/file.js

@@ -1,13 +1,14 @@
-import { unzip } from '../unzip';
+import { Buffer } from 'buffer';
 import crc32 from 'buffer-crc32';
 import QuickLRU from 'quick-lru';
 import htscodecs from '@jkbonfield/htscodecs';
-// @ts-expect-error
 import bzip2 from 'bzip2';
 import { XzReadableStream } from 'xz-decompress';
 import { CramMalformedError, CramUnimplementedError } from '../errors';
+// locals
+import { unzip } from '../unzip';
 import ransuncompress from '../rans';
-import { cramFileDefinition as cramFileDefinitionParser, getSectionParsers, } from './sectionParsers';
+import { cramFileDefinition, getSectionParsers, } from './sectionParsers';
 import CramContainer from './container';
 import { open } from '../io';
 import { parseItem, tinyMemoize } from './util';
@@ -20,18 +21,18 @@ 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?
     }
 }
 export default class CramFile {
@@ -65,10 +66,10 @@ export default class CramFile {
     }
     // memoized
     async getDefinition() {
-        const headbytes = Buffer.allocUnsafe(cramFileDefinitionParser.maxLength);
-        await this.file.read(headbytes, 0, cramFileDefinitionParser.maxLength, 0);
-        const definition = cramFileDefinitionParser.parser.parse(headbytes)
-            .result;
+        const { maxLength, parser } = cramFileDefinition();
+        const headbytes = Buffer.allocUnsafe(maxLength);
+        await this.file.read(headbytes, 0, maxLength, 0);
+        const definition = parser(headbytes).value;
         if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
             throw new CramUnimplementedError(`CRAM version ${definition.majorVersion} not supported`);
         }
@@ -99,19 +100,15 @@ export default class CramFile {
         await this.getSamHeader();
         return this.header;
     }
-    // memoize
-    async getSectionParsers() {
-        const { majorVersion } = await this.getDefinition();
-        return getSectionParsers(majorVersion);
-    }
     async getContainerById(containerNumber) {
-        const sectionParsers = await this.getSectionParsers();
+        const { majorVersion } = await this.getDefinition();
+        const sectionParsers = getSectionParsers(majorVersion);
         let position = sectionParsers.cramFileDefinition.maxLength;
         const { size: fileSize } = await 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) {
@@ -122,13 +119,12 @@ export default class CramFile {
             if (!currentHeader) {
                 throw new 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 = await this.readBlock(position);
                     if (block === undefined) {
                         return undefined;
@@ -155,7 +151,8 @@ export default class CramFile {
      * @returns {Promise[number]} the number of containers in the file
      */
     async containerCount() {
-        const sectionParsers = await this.getSectionParsers();
+        const { majorVersion } = await this.getDefinition();
+        const sectionParsers = getSectionParsers(majorVersion);
         const { size: fileSize } = await this.file.stat();
         const { cramContainerHeader1 } = sectionParsers;
         let containerCount = 0;
@@ -170,7 +167,7 @@ export default 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 = await this.readBlock(position);
                     if (block === undefined) {
                         return undefined;
@@ -190,7 +187,8 @@ export default class CramFile {
         return new CramContainer(this, position);
     }
     async readBlockHeader(position) {
-        const sectionParsers = await this.getSectionParsers();
+        const { majorVersion } = await this.getDefinition();
+        const sectionParsers = getSectionParsers(majorVersion);
         const { cramBlockHeader } = sectionParsers;
         const { size: fileSize } = await this.file.stat();
         if (position + cramBlockHeader.maxLength >= fileSize) {
@@ -231,12 +229,12 @@ export default class CramFile {
             let chunk;
             do {
                 chunk = bzip2.decompress(bits, size);
-                if (chunk != -1) {
+                if (chunk !== -1) {
                     Buffer.from(chunk).copy(outputBuffer, j);
                     j += chunk.length;
                     size -= chunk.length;
                 }
-            } while (chunk != -1);
+            } while (chunk !== -1);
         }
         else if (compressionMethod === 'lzma') {
             const decompressedResponse = new Response(new XzReadableStream(bufferToStream(inputBuffer)));
@@ -266,7 +264,7 @@ export default class CramFile {
     }
     async readBlock(position) {
         const { majorVersion } = await this.getDefinition();
-        const sectionParsers = await this.getSectionParsers();
+        const sectionParsers = getSectionParsers(majorVersion);
         const blockHeader = await this.readBlockHeader(position);
         if (blockHeader === undefined) {
             return undefined;