@gmod/cram 1.6.2 → 1.6.3

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

@@ -1 +1 @@
-{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.js"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,sBAAsB,GACvB,MAAM,cAAc,CAAA;AACrB,OAAO,SAAS,MAAM,SAAS,CAAA;AAC/B,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAEnC,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAAS;IAClD,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ;QACnC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;SACnC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE;YACnC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;SACpC;aAAM;YACL,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,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,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAAY,EAAE,MAAM;QAC7B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,SAAS,CACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,IAAI,SAAS,CAAA;QAChC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAAY,EAAE,MAAM;QAC9B,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE;YACtD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;SACF;QACD,MAAM,MAAM,GAAG,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,CAAC,CAAA;QACxD,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QACxB,OAAO,MAAM,CAAA;IACf,CAAC;CACF"}
+{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.js"],"names":[],"mappings":"AAAA,OAAO,EACL,sBAAsB,EACtB,kBAAkB,EAClB,sBAAsB,GACvB,MAAM,cAAc,CAAA;AACrB,OAAO,SAAS,MAAM,SAAS,CAAA;AAC/B,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAEnC,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAAS;IAClD,YAAY,UAAU,GAAG,EAAE,EAAE,QAAQ;QACnC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;YAC3B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;SACnC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE;YACnC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;SACpC;aAAM;YACL,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,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,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAAY,EAAE,MAAM;QAC7B,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,SAAS,CACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,IAAI,SAAS,CAAA;QAChC,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAAY,EAAE,MAAM;QAC9B,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE;YACtD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;SACF;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF"}

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

@@ -72,7 +72,7 @@ export default class CramContainerCompressionScheme {
         this.referenceRequired = !!content.preservation.RR;
         this.tagIdsDictionary = content.preservation.TD;
         this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
-        this.dataSeriesCodecCache = {};
+        this.dataSeriesCodecCache = new Map();
         this.tagCodecCache = {};
     }
     /**
@@ -97,17 +97,19 @@ export default class CramContainerCompressionScheme {
         return this.tagIdsDictionary[tagListId];
     }
     getCodecForDataSeries(dataSeriesName) {
-        if (!this.dataSeriesCodecCache[dataSeriesName]) {
+        let r = this.dataSeriesCodecCache.get(dataSeriesName);
+        if (r === undefined) {
             const encodingData = this.dataSeriesEncoding[dataSeriesName];
             if (encodingData) {
                 const dataType = dataSeriesTypes[dataSeriesName];
                 if (!dataType) {
                     throw new CramMalformedError(`data series name ${dataSeriesName} not defined in file compression header`);
                 }
-                this.dataSeriesCodecCache[dataSeriesName] = instantiateCodec(encodingData, dataType);
+                r = instantiateCodec(encodingData, dataType);
+                this.dataSeriesCodecCache.set(dataSeriesName, r);
             }
         }
-        return this.dataSeriesCodecCache[dataSeriesName];
+        return r;
     }
     toJSON() {
         const data = {};

package/esm/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,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,WAAW,CAAA;AAE5C,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,EAAE,EAAE,QAAQ;IACZ,EAAE,EAAE,QAAQ;CACb,CAAA;AAED,SAAS,uBAAuB,CAAC,SAAS;IACxC,MAAM,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,MAAM,CAAC,OAAO,OAAO,8BAA8B;IACjD,YAAY,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,cAAc,CAAC,OAAO;QACpB,IAAI,CAAC,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,EAAE;YAChC,MAAM,YAAY,GAAG,IAAI,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC9C,IAAI,YAAY,EAAE;gBAChB,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,GAAG,gBAAgB,CAC5C,YAAY,EACZ,WAAW,CACZ,CAAA;aACF;SACF;QACD,OAAO,IAAI,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;IACpC,CAAC;IAED;;;;OAIG;IACH,WAAW,CAAC,SAAS;QACnB,OAAO,IAAI,CAAC,gBAAgB,CAAC,SAAS,CAAC,CAAA;IACzC,CAAC;IAED,qBAAqB,CAAC,cAAc;QAClC,IAAI,CAAC,GAAG,IAAI,CAAC,oBAAoB,CAAC,GAAG,CAAC,cAAc,CAAC,CAAA;QACrD,IAAI,CAAC,KAAK,SAAS,EAAE;YACnB,MAAM,YAAY,GAAG,IAAI,CAAC,kBAAkB,CAAC,cAAc,CAAC,CAAA;YAC5D,IAAI,YAAY,EAAE;gBAChB,MAAM,QAAQ,GAAG,eAAe,CAAC,cAAc,CAAC,CAAA;gBAChD,IAAI,CAAC,QAAQ,EAAE;oBACb,MAAM,IAAI,kBAAkB,CAC1B,oBAAoB,cAAc,yCAAyC,CAC5E,CAAA;iBACF;gBACD,CAAC,GAAG,gBAAgB,CAAC,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,MAAM;QACJ,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;YAC5B,IAAI,QAAQ,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE;gBACpB,OAAM;aACP;YACD,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAA;QACnB,CAAC,CAAC,CAAA;QACF,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}

package/esm/cramFile/file.js

@@ -9,6 +9,20 @@ import CramContainer from './container';
 import { open } from '../io';
 import { parseItem, tinyMemoize } from './util';
 import { parseHeaderText } from '../sam';
+//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+function getEndianness() {
+    let uInt32 = new Uint32Array([0x11223344]);
+    let 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?
+    }
+}
 export default class CramFile {
     /**
      * @param {object} args
@@ -37,6 +51,9 @@ export default class CramFile {
         this.featureCache = new LRU({
             maxSize: this.options.cacheSize,
         });
+        if (getEndianness() > 0) {
+            throw new Error('Detected big-endian machine, may be unable to run');
+        }
     }
     toString() {
         if (this.file.filename) {

package/esm/cramFile/file.js.map

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

@@ -1,17 +1,17 @@
 import Long from 'long';
-import { CramMalformedError, CramUnimplementedError } from '../../errors';
+import { CramMalformedError } from '../../errors';
 import CramRecord from '../record';
 import Constants from '../constants';
 /**
  * given a Buffer, read a string up to the first null character
  * @private
  */
-function readNullTerminatedStringFromBuffer(buffer) {
-    const zeroOffset = buffer.indexOf(0);
-    if (zeroOffset === -1) {
-        return buffer.toString('utf8');
+function readNullTerminatedString(buffer) {
+    let r = '';
+    for (let 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
@@ -19,67 +19,86 @@ function readNullTerminatedStringFromBuffer(buffer) {
  */
 function parseTagValueArray(buffer) {
     const arrayType = String.fromCharCode(buffer[0]);
-    const length = buffer.readInt32LE(1);
-    const 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 CramMalformedError(`invalid tag value array type '${arrayType}'`);
-    }
-    const [getMethod, itemSize] = schema;
+    const length = Int32Array.from(buffer.slice(1))[0];
     const array = new Array(length);
-    let offset = 5;
-    for (let i = 0; i < length; i += 1) {
-        array[i] = buffer[getMethod](offset);
-        offset += itemSize;
+    buffer = buffer.slice(5);
+    if (arrayType === 'c') {
+        const arr = new Int8Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'C') {
+        const arr = new Uint8Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 's') {
+        const arr = new Int16Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'S') {
+        const arr = new Uint16Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'i') {
+        const arr = new Int32Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'I') {
+        const arr = new Uint32Array(buffer.buffer);
+        for (let i = 0; i < length; i += 1) {
+            array[i] = arr[i];
+        }
+    }
+    else if (arrayType === 'f') {
+        const arr = new Float32Array(buffer.buffer);
+        for (let 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') {
-        const val = Long.fromBytesLE(buffer);
-        if (val.greaterThan(Number.MAX_SAFE_INTEGER) ||
-            val.lessThan(Number.MIN_SAFE_INTEGER)) {
-            throw new CramUnimplementedError('integer overflow');
-        }
-        return val.toNumber();
+        return Long.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') {
-        const hex = readNullTerminatedStringFromBuffer(buffer);
-        return Number.parseInt(hex.replace(/^0x/, ''), 16);
+        return Number.parseInt(readNullTerminatedString(buffer).replace(/^0x/, ''), 16);
     }
     if (tagType === 'B') {
         return parseTagValueArray(buffer);
@@ -152,21 +171,6 @@ 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
-            const termIndex = thing.indexOf(0);
-            return String.fromCharCode(...thing.slice(0, termIndex));
-        }
-        return String.fromCharCode(...thing);
-    }
-    return String(thing);
-}
 export default function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
     const cramRecord = new CramRecord();
     cramRecord.flags = decodeDataSeries('BF');
@@ -189,7 +193,7 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
     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()) {
@@ -197,7 +201,7 @@ export default function decodeRecord(slice, decodeDataSeries, compressionScheme,
         const 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/esm/cramFile/slice/decodeRecord.js.map

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package/esm/cramFile/slice/index.js

@@ -242,18 +242,22 @@ export default class CramSlice {
             }
         }
         // tracks the read position within the block. codec.decode() methods
-        // advance the byte and bit positions in the cursor as they decode data
-        // note that we are only decoding a single block here, the core data block
+        // advance the byte and bit positions in the cursor as they decode
+        // data note that we are only decoding a single block here, the core
+        // data block
         const coreDataBlock = await this.getCoreDataBlock();
         const cursors = {
             lastAlignmentStart: sliceHeader.content.refSeqStart || 0,
             coreBlock: { bitPosition: 7, bytePosition: 0 },
             externalBlocks: {
+                map: new Map(),
                 getCursor(contentId) {
-                    if (!this[contentId]) {
-                        this[contentId] = { bitPosition: 7, bytePosition: 0 };
+                    let r = this.map.get(contentId);
+                    if (r === undefined) {
+                        r = { bitPosition: 7, bytePosition: 0 };
+                        this.map.set(contentId, r);
                     }
-                    return this[contentId];
+                    return r;
                 },
             },
         };
@@ -286,8 +290,8 @@ export default class CramSlice {
                 }
             }
         }
-        // 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 (let i = 0; i < records.length; i += 1) {
             const { mateRecordNumber } = records[i];
             if (mateRecordNumber >= 0) {

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

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/cram",
-  "version": "1.6.2",
+  "version": "1.6.3",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",

package/src/cramFile/codecs/byteArrayLength.js

@@ -23,7 +23,7 @@ export default class ByteArrayStopCodec extends CramCodec {
     )
 
     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,

package/src/cramFile/codecs/byteArrayStop.js

@@ -44,7 +44,6 @@ 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)
   }
 }

package/src/cramFile/codecs/external.js

@@ -47,8 +47,6 @@ export default class ExternalCodec extends CramCodec {
         '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++]
   }
 }

package/src/cramFile/container/compressionScheme.js

@@ -82,7 +82,7 @@ export default class CramContainerCompressionScheme {
     this.tagIdsDictionary = content.preservation.TD
     this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM)
 
-    this.dataSeriesCodecCache = {}
+    this.dataSeriesCodecCache = new Map()
     this.tagCodecCache = {}
   }
 
@@ -113,7 +113,8 @@ export default class CramContainerCompressionScheme {
   }
 
   getCodecForDataSeries(dataSeriesName) {
-    if (!this.dataSeriesCodecCache[dataSeriesName]) {
+    let r = this.dataSeriesCodecCache.get(dataSeriesName)
+    if (r === undefined) {
       const encodingData = this.dataSeriesEncoding[dataSeriesName]
       if (encodingData) {
         const dataType = dataSeriesTypes[dataSeriesName]
@@ -122,13 +123,11 @@ export default class CramContainerCompressionScheme {
             `data series name ${dataSeriesName} not defined in file compression header`,
           )
         }
-        this.dataSeriesCodecCache[dataSeriesName] = instantiateCodec(
-          encodingData,
-          dataType,
-        )
+        r = instantiateCodec(encodingData, dataType)
+        this.dataSeriesCodecCache.set(dataSeriesName, r)
       }
     }
-    return this.dataSeriesCodecCache[dataSeriesName]
+    return r
   }
 
   toJSON() {

package/src/cramFile/file.js

@@ -14,6 +14,19 @@ import CramContainer from './container'
 import { open } from '../io'
 import { parseItem, tinyMemoize } from './util'
 import { parseHeaderText } from '../sam'
+//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+function getEndianness() {
+  let uInt32 = new Uint32Array([0x11223344])
+  let 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?
+  }
+}
 
 export default class CramFile {
   /**
@@ -44,6 +57,9 @@ export default class CramFile {
     this.featureCache = new LRU({
       maxSize: this.options.cacheSize,
     })
+    if (getEndianness() > 0) {
+      throw new Error('Detected big-endian machine, may be unable to run')
+    }
   }
 
   toString() {