npm - @gmod/cram - Versions diffs - 3.0.3 → 3.0.5 - Mend

@gmod/cram 3.0.3 → 3.0.5

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (106) hide show

package/dist/craiIndex.d.ts +3 -5
package/dist/craiIndex.js +28 -30
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/byteArrayLength.js +3 -6
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/byteArrayStop.d.ts +0 -1
package/dist/cramFile/codecs/byteArrayStop.js +0 -6
package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
package/dist/cramFile/codecs/external.js +0 -1
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.js +1 -2
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/container/compressionScheme.d.ts +1 -1
package/dist/cramFile/container/compressionScheme.js +12 -4
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.js +3 -1
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +1 -1
package/dist/cramFile/file.js +11 -12
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.js +1 -7
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +6 -11
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.d.ts +3 -2
package/dist/cramFile/slice/index.js +10 -16
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.js.map +1 -1
package/dist/indexedCramFile.js +0 -3
package/dist/indexedCramFile.js.map +1 -1
package/dist/rans/d04.js +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/d14.js +1 -1
package/dist/rans/d14.js.map +1 -1
package/dist/rans/decoding.js +1 -1
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/frequencies.js +1 -1
package/dist/rans/frequencies.js.map +1 -1
package/dist/rans/index.js +1 -1
package/dist/rans/index.js.map +1 -1
package/esm/craiIndex.d.ts +3 -5
package/esm/craiIndex.js +63 -64
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.js +3 -6
package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.d.ts +0 -1
package/esm/cramFile/codecs/byteArrayStop.js +0 -6
package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
package/esm/cramFile/codecs/external.js +0 -1
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/getBits.js.map +1 -1
package/esm/cramFile/codecs/huffman.js +1 -2
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/container/compressionScheme.d.ts +1 -1
package/esm/cramFile/container/compressionScheme.js +12 -4
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.js +3 -1
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +1 -1
package/esm/cramFile/file.js +10 -11
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.js +1 -7
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +6 -8
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.d.ts +3 -2
package/esm/cramFile/slice/index.js +10 -16
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.js.map +1 -1
package/esm/indexedCramFile.js +0 -3
package/esm/indexedCramFile.js.map +1 -1
package/esm/rans/d04.js +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/d14.js +1 -1
package/esm/rans/d14.js.map +1 -1
package/esm/rans/decoding.js +1 -1
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/frequencies.js +1 -1
package/esm/rans/frequencies.js.map +1 -1
package/esm/rans/index.js +1 -1
package/esm/rans/index.js.map +1 -1
package/package.json +10 -10
package/src/craiIndex.ts +82 -81
package/src/cramFile/codecs/byteArrayLength.ts +3 -8
package/src/cramFile/codecs/byteArrayStop.ts +0 -12
package/src/cramFile/codecs/external.ts +1 -2
package/src/cramFile/codecs/getBits.ts +1 -1
package/src/cramFile/codecs/huffman.ts +11 -12
package/src/cramFile/container/compressionScheme.ts +38 -31
package/src/cramFile/container/index.ts +3 -1
package/src/cramFile/file.ts +10 -11
package/src/cramFile/record.ts +3 -10
package/src/cramFile/sectionParsers.ts +4 -4
package/src/cramFile/slice/decodeRecord.ts +22 -32
package/src/cramFile/slice/index.ts +16 -25
package/src/cramFile/util.ts +36 -35
package/src/indexedCramFile.ts +1 -4
package/src/rans/d04.ts +1 -1
package/src/rans/d14.ts +1 -1
package/src/rans/decoding.ts +1 -1
package/src/rans/frequencies.ts +1 -1
package/src/rans/index.ts +1 -1

package/dist/cramFile/codecs/byteArrayLength.js CHANGED Viewed

@@ -9,9 +9,6 @@ class ByteArrayStopCodec extends _base_1.default {
     constructor(parameters, dataType, instantiateCodec) {
         super(parameters, dataType);
         this.instantiateCodec = instantiateCodec;
-        if (dataType !== 'byteArray') {
-            throw new TypeError(`byteArrayLength does not support data type ${dataType}`);
-        }
     }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const lengthCodec = this._getLengthCodec();
@@ -35,7 +32,7 @@ class ByteArrayStopCodec extends _base_1.default {
     }
 }
 exports.default = ByteArrayStopCodec;
-'_getLengthCodec _getDataCodec'
-    .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(ByteArrayStopCodec, method));
+'_getLengthCodec _getDataCodec'.split(' ').forEach(method => {
+    (0, util_1.tinyMemoize)(ByteArrayStopCodec, method);
+});
 //# sourceMappingURL=byteArrayLength.js.map

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

	@@ -1 +1 @@
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package/dist/cramFile/codecs/byteArrayStop.d.ts CHANGED Viewed

@@ -3,7 +3,6 @@ import CramSlice from '../slice';
 import { CramFileBlock } from '../file';
 import { ByteArrayStopCramEncoding } from '../encoding';
 export default class ByteArrayStopCodec extends CramCodec<'byteArray', ByteArrayStopCramEncoding['parameters']> {
-    constructor(parameters: ByteArrayStopCramEncoding['parameters'], dataType: 'byteArray');
     decode(slice: CramSlice, coreDataBlock: CramFileBlock, blocksByContentId: Record<number, CramFileBlock>, cursors: Cursors): Buffer;
     _decodeByteArray(contentBlock: CramFileBlock, cursor: Cursor): Buffer;
 }

package/dist/cramFile/codecs/byteArrayStop.js CHANGED Viewed

@@ -7,12 +7,6 @@ const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const getBits_1 = require("./getBits");
 class ByteArrayStopCodec extends _base_1.default {
-    constructor(parameters, dataType) {
-        super(parameters, dataType);
-        if (dataType !== 'byteArray') {
-            throw new TypeError(`byteArrayStop codec does not support data type ${dataType}`);
-        }
-    }
     decode(slice, coreDataBlock, blocksByContentId, cursors) {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];

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

	@@ -1 +1 @@
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package/dist/cramFile/codecs/external.js CHANGED Viewed

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/unbound-method */
 const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const util_1 = require("../util");

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":";;;;;AAAA,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,CAAE,CAAA;IACrD,CAAC;CACF;AA3DD,gCA2DC"}

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

	@@ -1 +1 @@
1	- {"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAEA,0BAyBC;AA3BD,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,SAAgB,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX,CAAC;QACD,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;IACH,CAAC;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;QACtC,yDAAyD;QACzD,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,~~CAAC~~,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;~~QAC5D~~,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QAC1B,CAAC;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
1	+ {"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":";;;AAEA,0BAyBC;AA3BD,MAAa,sBAAuB,SAAQ,KAAK;CAAG;AAApD,wDAAoD;AAEpD,SAAgB,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX,CAAC;QACD,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;IACH,CAAC;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;QACtC,yDAAyD;QACzD,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAE,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC7D,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QAC1B,CAAC;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}

package/dist/cramFile/codecs/huffman.js CHANGED Viewed

@@ -3,7 +3,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-/* eslint-disable @typescript-eslint/unbound-method */
 const errors_1 = require("../../errors");
 const _base_1 = __importDefault(require("./_base"));
 const getBits_1 = require("./getBits");
@@ -37,7 +36,7 @@ class HuffmanIntCodec extends _base_1.default {
     buildCodeBook() {
         // parse the parameters together into a `codes` data structure
         let codes = new Array(this.parameters.numCodes);
-        for (let i = 0; i < this.parameters.numCodes; i += 1) {
+        for (let i = 0; i < this.parameters.numCodes; i++) {
             codes[i] = {
                 symbol: this.parameters.symbols[i],
                 bitLength: this.parameters.bitLengths[i],

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

	@@ -1 +1 @@
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1	+ 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package/dist/cramFile/container/compressionScheme.d.ts CHANGED Viewed

@@ -59,7 +59,7 @@ export default class CramContainerCompressionScheme {
      * @param {number} tagListId ID of the tag list to fetch from the tag dictionary
      * @private
      */
-    getTagNames(tagListId: number): string[];
+    getTagNames(tagListId: number): string[] | undefined;
     getCodecForDataSeries<TDataSeries extends DataSeriesEncodingKey>(dataSeriesName: TDataSeries): CramCodec<DataSeriesTypes[TDataSeries]> | undefined;
     toJSON(): any;
 }

package/dist/cramFile/container/compressionScheme.js CHANGED Viewed

@@ -84,13 +84,19 @@ class CramContainerCompressionScheme {
      * @private
      */
     getCodecForTag(tagName) {
-        if (!this.tagCodecCache[tagName]) {
+        const test = this.tagCodecCache[tagName];
+        if (!test) {
             const encodingData = this.tagEncoding[tagName];
-            if (encodingData) {
-                this.tagCodecCache[tagName] = (0, codecs_1.instantiateCodec)(encodingData, 'byteArray');
+            if (!encodingData) {
+                throw new Error('Error, no tag encoding');
             }
+            const ret = (0, codecs_1.instantiateCodec)(encodingData, 'byteArray');
+            this.tagCodecCache[tagName] = ret;
+            return ret;
+        }
+        else {
+            return test;
         }
-        return this.tagCodecCache[tagName];
     }
     /**
      *
@@ -104,8 +110,10 @@ class CramContainerCompressionScheme {
         let r = this.dataSeriesCodecCache[dataSeriesName];
         if (r === undefined) {
             const encodingData = this.dataSeriesEncoding[dataSeriesName];
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             if (encodingData) {
                 const dataType = dataSeriesTypes[dataSeriesName];
+                // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
                 if (!dataType) {
                     throw new errors_1.CramMalformedError(`data series name ${dataSeriesName} not defined in file compression header`);
                 }

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

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/cramFile/container/index.js CHANGED Viewed

@@ -111,5 +111,7 @@ class CramContainer {
 exports.default = CramContainer;
 'getHeader getCompressionHeaderBlock getCompressionScheme'
     .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(CramContainer, method));
+    .forEach(method => {
+    (0, util_1.tinyMemoize)(CramContainer, method);
+});
 //# sourceMappingURL=index.js.map

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

	@@ -1 +1 @@
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1	+ {"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;IAChB,IAAA,kBAAW,EAAC,aAAa,EAAE,MAAM,CAAC,CAAA;AACpC,CAAC,CAAC,CAAA"}

package/dist/cramFile/file.d.ts CHANGED Viewed

@@ -75,7 +75,7 @@ export default class CramFile {
             offset: number;
             value: T;
         };
-    }, position: number, size?: number, preReadBuffer?: undefined): Promise<(T & {
+    }, position: number, size?: number, preReadBuffer?: Buffer): Promise<(T & {
         _endPosition: number;
         _size: number;
     }) | undefined>;

package/dist/cramFile/file.js CHANGED Viewed

@@ -13,7 +13,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const buffer_1 = require("buffer");
-const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
+const crc32_1 = __importDefault(require("crc/crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const htscodecs_1 = __importDefault(require("@jkbonfield/htscodecs"));
 const bzip2_1 = __importDefault(require("bzip2"));
@@ -59,10 +59,9 @@ class CramFile {
             checkSequenceMD5: args.checkSequenceMD5,
             cacheSize: (_a = args.cacheSize) !== null && _a !== void 0 ? _a : 20000,
         };
-        // cache of features in a slice, keyed by the
-        // slice offset. caches all of the features in a slice, or none.
-        // the cache is actually used by the slice object, it's just
-        // kept here at the level of the file
+        // cache of features in a slice, keyed by the slice offset. caches all of
+        // the features in a slice, or none. the cache is actually used by the
+        // slice object, it's just kept here at the level of the file
         this.featureCache = new quick_lru_1.default({
             maxSize: this.options.cacheSize,
         });
@@ -165,7 +164,7 @@ class CramFile {
         return __awaiter(this, void 0, void 0, function* () {
             const b = buffer_1.Buffer.allocUnsafe(length);
             yield this.file.read(b, 0, length, position);
-            const calculatedCrc32 = buffer_crc32_1.default.unsigned(b);
+            const calculatedCrc32 = crc32_1.default.unsigned(b);
             if (calculatedCrc32 !== recordedCrc32) {
                 throw new errors_1.CramMalformedError(`crc mismatch in ${description}: recorded CRC32 = ${recordedCrc32}, but calculated CRC32 = ${calculatedCrc32}`);
             }
@@ -227,7 +226,7 @@ class CramFile {
         });
     }
     _parseSection(section_1, position_1) {
-        return __awaiter(this, arguments, void 0, function* (section, position, size = section.maxLength, preReadBuffer = undefined) {
+        return __awaiter(this, arguments, void 0, function* (section, position, size = section.maxLength, preReadBuffer) {
             let buffer;
             if (preReadBuffer) {
                 buffer = preReadBuffer;
@@ -274,8 +273,8 @@ class CramFile {
             }
             else if (compressionMethod === 'rans') {
                 (0, rans_1.default)(inputBuffer, outputBuffer);
-                //htscodecs r4x8 is slower, but compatible.
-                //htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
+                // htscodecs r4x8 is slower, but compatible.
+                // htscodecs.r4x8_uncompress(inputBuffer, outputBuffer);
             }
             else if (compressionMethod === 'rans4x16') {
                 htscodecs_1.default.r4x16_uncompress(inputBuffer, outputBuffer);
@@ -338,7 +337,7 @@ class CramFile {
     }
 }
 exports.default = CramFile;
-'getDefinition getSectionParsers getSamHeader'
-    .split(' ')
-    .forEach(method => (0, util_1.tinyMemoize)(CramFile, method));
+'getDefinition getSectionParsers getSamHeader'.split(' ').forEach(method => {
+    (0, util_1.tinyMemoize)(CramFile, method);
+});
 //# sourceMappingURL=file.js.map

package/dist/cramFile/file.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/cramFile/record.js CHANGED Viewed

@@ -81,10 +81,7 @@ function decodeReadSequence(cramRecord, refRegion) {
             }
             else if (currentReadFeature < cramRecord.readFeatures.length) {
                 // put down a chunk of sequence up to the next read feature
-                const chunk = refRegion.seq.slice(regionPos, regionPos +
-                    cramRecord.readFeatures[currentReadFeature].pos -
-                    bases.length -
-                    1);
+                const chunk = refRegion.seq.slice(regionPos, regionPos + feature.pos - bases.length - 1);
                 bases += chunk;
                 regionPos += chunk.length;
             }
@@ -111,9 +108,6 @@ const baseNumbers = {
     N: 4,
 };
 function decodeBaseSubstitution(cramRecord, refRegion, compressionScheme, readFeature) {
-    if (!refRegion) {
-        return;
-    }
     // decode base substitution code using the substitution matrix
     const refCoord = readFeature.refPos - refRegion.start;
     const refBase = refRegion.seq.charAt(refCoord);

package/dist/cramFile/record.js.map CHANGED Viewed

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

@@ -1,10 +1,6 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = decodeRecord;
-const long_1 = __importDefault(require("long"));
 const errors_1 = require("../../errors");
 const record_1 = require("../record");
 const sectionParsers_1 = require("../sectionParsers");
@@ -83,7 +79,7 @@ function parseTagData(tagType, buffer) {
         return String.fromCharCode(buffer[0]);
     }
     if (tagType === 'I') {
-        return long_1.default.fromBytesLE(buffer).toNumber();
+        return new Uint32Array(buffer.buffer)[0];
     }
     if (tagType === 'i') {
         return new Int32Array(buffer.buffer)[0];
@@ -256,12 +252,11 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         const tagId = TN[i];
         const tagName = tagId.slice(0, 2);
         const tagType = tagId.slice(2, 3);
-        const tagCodec = compressionScheme.getCodecForTag(tagId);
-        if (!tagCodec) {
-            throw new errors_1.CramMalformedError(`no codec defined for auxiliary tag ${tagId}`);
-        }
-        const tagData = tagCodec.decode(slice, coreDataBlock, blocksByContentId, cursors);
-        tags[tagName] = parseTagData(tagType, tagData);
+        const tagData = compressionScheme
+            .getCodecForTag(tagId)
+            .decode(slice, coreDataBlock, blocksByContentId, cursors);
+        tags[tagName] =
+            typeof tagData === 'number' ? tagData : parseTagData(tagType, tagData);
     }
     let readFeatures;
     let lengthOnRef;