@gmod/tabix 1.5.6 → 1.5.8

package/CHANGELOG.md

@@ -1,45 +1,45 @@
-## [1.5.6](https://github.com/GMOD/tabix-js/compare/v1.5.5...v1.5.6) (2023-02-28)
+## [1.5.8](https://github.com/GMOD/tabix-js/compare/v1.5.7...v1.5.8) (2023-03-24)
 
 
 
-- Add fix for fileOffset being stable in presence of Unicode characters (#137)
+- Make yieldTime optional
 
-## [1.5.5](https://github.com/GMOD/tabix-js/compare/v1.5.4...v1.5.5) (2022-12-17)
+## [1.5.7](https://github.com/GMOD/tabix-js/compare/v1.5.6...v1.5.7) (2023-03-24)
 
+- Add yieldTime parameter
+- Improve typescripting
 
+## [1.5.6](https://github.com/GMOD/tabix-js/compare/v1.5.5...v1.5.6) (2023-02-28)
 
-- Use es2015 for nodejs build
+- Add fix for fileOffset being stable in presence of Unicode characters (#137)
 
-## [1.5.4](https://github.com/GMOD/tabix-js/compare/v1.5.3...v1.5.4) (2022-07-18)
+## [1.5.5](https://github.com/GMOD/tabix-js/compare/v1.5.4...v1.5.5) (2022-12-17)
 
+- Use es2015 for nodejs build
 
+## [1.5.4](https://github.com/GMOD/tabix-js/compare/v1.5.3...v1.5.4) (2022-07-18)
 
 - Bump generic-filehandle 2->3
 
 ## [1.5.3](https://github.com/GMOD/tabix-js/compare/v1.5.2...v1.5.3) (2022-04-25)
 
-
-
 - Fix esm module build to use ESM instead of CJS
 
 <a name="1.5.2"></a>
-## [1.5.2](https://github.com/GMOD/tabix-js/compare/v1.5.1...v1.5.2) (2021-12-15)
-
 
+## [1.5.2](https://github.com/GMOD/tabix-js/compare/v1.5.1...v1.5.2) (2021-12-15)
 
 - Change typescript signature of lineCallback from Promise<void> to void
 
 <a name="1.5.1"></a>
-## [1.5.1](https://github.com/GMOD/tabix-js/compare/v1.5.0...v1.5.1) (2021-12-15)
-
 
+## [1.5.1](https://github.com/GMOD/tabix-js/compare/v1.5.0...v1.5.1) (2021-12-15)
 
 - Add esm module with less babelification for smaller bundle size
 
 <a name="1.5.0"></a>
-# [1.5.0](https://github.com/GMOD/tabix-js/compare/v1.4.6...v1.5.0) (2020-12-11)
-
 
+# [1.5.0](https://github.com/GMOD/tabix-js/compare/v1.4.6...v1.5.0) (2020-12-11)
 
 - Use TextDecoder for chunk decoding for small speedup
 - Use canMergeChunks logic to avoid too large of chunks being used
@@ -49,14 +49,16 @@
 
 ## [1.4.6](https://github.com/GMOD/tabix-js/compare/v1.4.5...v1.4.6) (2020-04-30)
 
-- Fix regression with browser only version of tabix-js not being able to parse results in 1.4.5
+- Fix regression with browser only version of tabix-js not being able to parse
+  results in 1.4.5
 
 <a name="1.4.5"></a>
 
 ## [1.4.5](https://github.com/GMOD/tabix-js/compare/v1.4.4...v1.4.5) (2020-04-28)
 
-- Remove the filehandle size() call because this is unnecessary and would indicate a corrupt index,
-  and because it additionally has a CORS configuration overhead
+- Remove the filehandle size() call because this is unnecessary and would
+  indicate a corrupt index, and because it additionally has a CORS configuration
+  overhead
 
 <a name="1.4.4"></a>
 
@@ -69,7 +71,8 @@
 ## [1.4.3](https://github.com/GMOD/tabix-js/compare/v1.4.2...v1.4.3) (2020-02-04)
 
 - Fix optional param for constructor for typescript
-- Update method of calculating fileOffset based IDs using updated @gmod/bgzf-filehandle
+- Update method of calculating fileOffset based IDs using updated
+  @gmod/bgzf-filehandle
 
 <a name="1.4.2"></a>
 
@@ -121,11 +124,13 @@
 
 ## [1.1.8](https://github.com/GMOD/tabix-js/compare/v1.1.7...v1.1.8) (2019-06-06)
 
-- Add a fix for a bgzf unzipping thing that could result in duplicate features being returned
+- Add a fix for a bgzf unzipping thing that could result in duplicate features
+  being returned
 
 ## [1.1.7](https://github.com/GMOD/tabix-js/compare/v1.1.6...v1.1.7) (2019-06-04)
 
-- Removed chunk merging from header file parsing which now results in smaller bgzf unzip calls being streamed out to clients
+- Removed chunk merging from header file parsing which now results in smaller
+  bgzf unzip calls being streamed out to clients
 
 ## [1.1.6](https://github.com/GMOD/tabix-js/compare/v1.1.5...v1.1.6) (2019-05-31)
 
@@ -134,7 +139,8 @@
 
 ## [1.1.5](https://github.com/GMOD/tabix-js/compare/v1.1.4...v1.1.5) (2019-03-05)
 
-- Fix parsing on a tabix file that should be csi files (e.g. too long of chromosomes)
+- Fix parsing on a tabix file that should be csi files (e.g. too long of
+  chromosomes)
 
 ## [1.1.4](https://github.com/GMOD/tabix-js/compare/v1.1.3...v1.1.4) (2019-02-23)
 
@@ -142,7 +148,8 @@
 
 ## [1.1.3](https://github.com/GMOD/tabix-js/compare/v1.1.2...v1.1.3) (2018-11-23)
 
-- Change to es6-promisify and quick-lru which can be babelified to IE11 (util.promisify and lru-cache used Object.defineProperty('length', ...))
+- Change to es6-promisify and quick-lru which can be babelified to IE11
+  (util.promisify and lru-cache used Object.defineProperty('length', ...))
 
 ## [1.1.2](https://github.com/GMOD/tabix-js/compare/v1.1.1...v1.1.2) (2018-10-26)
 

package/README.md

@@ -14,7 +14,7 @@ Read Tabix-indexed files using either .tbi or .csi indexes.
 
 ### Importing the module
 
-```js
+```typescript
 // import with require in node.js
 const { TabixIndexedFile } = require('@gmod/tabix')
 
@@ -28,7 +28,7 @@ Basic usage of TabixIndexedFile under node.js supplies a path and optionally a
 tbiPath to the constructor. If no tbiPath is supplied, it assumes that the
 path+'.tbi' is the location of the tbiPath.
 
-```
+```typescript
 // basic usage under node.js provides a file path on the filesystem to bgzipped file
 // it assumes the tbi file is path+'.tbi' if no tbiPath is supplied
 const tbiIndexed = new TabixIndexedFile({
@@ -43,7 +43,7 @@ The renameRefSeqs callback makes it so that you can use
 file.getLines('1',0,100,...) even when the file itself contains names like
 'chr1' (can also do the reverse by customizing the renameRefSeqs callback)
 
-```
+```typescript
 // can also open tabix files that have a .csi index
 // note also usage of renameRefSeqs callback to trim chr off the chr names
 const csiIndexed = new TabixIndexedFile({
@@ -59,12 +59,12 @@ The basic usage of fetching remote files is done by supplying a
 [generic-filehandle](https://github.com/GMOD/generic-filehandle) module
 RemoteFile filehandle, as seen below
 
-```
+```typescript
 // use a remote file or other filehandle, note RemoteFile comes from https://github.com/GMOD/generic-filehandle
-const {RemoteFile} = require('generic-filehandle')
+const { RemoteFile } = require('generic-filehandle')
 const remoteTbiIndexed = new TabixIndexedFile({
   filehandle: new RemoteFile('http://yourhost/file.vcf.gz'),
-  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi') // can also be csiFilehandle
+  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi'), // can also be csiFilehandle
 })
 ```
 
@@ -72,12 +72,12 @@ This works in both the browser and in node.js, but note that in node.js you have
 to also supply a custom fetch function to the RemoteFile constructor e.g. like
 this
 
-```
+```typescript
 // for node.js you have to manually supply a fetch function e.g. node-fetch to RemoteFile
 const fetch = require('node-fetch')
 const remoteTbiIndexedForNodeJs = new TabixIndexedFile({
-  filehandle: new RemoteFile('http://yourhost/file.vcf.gz', {fetch}),
-  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi', {fetch}) // can also be csiFilehandle
+  filehandle: new RemoteFile('http://yourhost/file.vcf.gz', { fetch }),
+  tbiFilehandle: new RemoteFile('http://yourhost/file.vcf.gz.tbi', { fetch }), // can also be csiFilehandle
 })
 ```
 
@@ -91,13 +91,12 @@ Important: the `start` and `end` values that are supplied to `getLines` are
 0-based half-open coordinates. This is different from the 1-based values that
 are supplied to the tabix command line tool
 
-```
+```typescript
 // iterate over lines in the specified region
 const lines = []
-await tbiIndexed.getLines('ctgA',200,300, function(line, fileOffset) {
-    lines.push(line)
+await tbiIndexed.getLines('ctgA', 200, 300, function (line, fileOffset) {
+  lines.push(line)
 })
-
 ```
 
 After running this, your `lines` array would contain an array of lines from the
@@ -106,14 +105,13 @@ file that match your query range
 You can also supply some extra arguments to getLines with this format, but these
 are sort of obscure and only used in some circumstances
 
-```
+```typescript
 const lines = []
 const aborter = new AbortController()
-await tbiIndexed.getLines('ctgA',200,300, {
+await tbiIndexed.getLines('ctgA', 200, 300, {
   lineCallback: (line, fileOffset) => lines.push(line),
-  signal: aborter.signal // an optional AbortSignal from an AbortController
+  signal: aborter.signal, // an optional AbortSignal from an AbortController
 })
-
 ```
 
 After running the above demo, lines is now an array of strings, containing the
@@ -129,7 +127,7 @@ Notes about the returned values of `getLines`:
 - if getLines is called with an undefined `end` parameter it gets all lines from
   start going to the end of the contig e.g.
 
-```
+```typescript
 const lines = []
 await tbiIndexed.getLines('ctgA', 0, undefined, line=>lines.push(line))`
 console.log(lines)
@@ -137,18 +135,17 @@ console.log(lines)
 
 ### lineCount
 
-```
+```typescript
 // get the approximate number of data lines in the
 // file for the given reference sequence, excluding header, comment, and whitespace lines
 // uses the extra bin from tabix
 const numLines = await tbiIndexed.lineCount('ctgA')
 // or const numLines = await tbiIndexed.lineCount('ctgA', { signal: aborter.signal })
-
 ```
 
 ### getHeader
 
-```
+```typescript
 // get the "header text" string from the file, which is the first contiguous
 // set of lines in the file that all start with a "meta" character (usually #)
 const headerText = await tbiIndexed.getHeader()
@@ -157,7 +154,7 @@ const headerText = await tbiIndexed.getHeader()
 
 #### getHeaderBuffer
 
-```
+```typescript
 // or if you want a nodejs Buffer object instead, there is getHeaderBuffer()
 const headerBuffer = await tbiIndexed.getHeaderBuffer()
 // or const headerBuffer = await tbiIndexed.getHeaderBuffer({ signal: aborter.signal })

package/dist/csi.d.ts

@@ -8,22 +8,14 @@ export default class CSI extends IndexFile {
     private minShift;
     constructor(args: any);
     lineCount(refName: string, opts?: Options): Promise<number>;
-    indexCov(): Promise<never[]>;
-    parseAuxData(bytes: Buffer, offset: number, auxLength: number): {
-        refIdToName: never[];
-        refNameToId: {};
-        skipLines?: undefined;
-        metaChar?: undefined;
-        columnNumbers?: undefined;
-        format?: undefined;
-        coordinateType?: undefined;
-    } | {
+    indexCov(): Promise<void>;
+    parseAuxData(bytes: Buffer, offset: number): {
         refIdToName: string[];
         refNameToId: {
             [key: string]: number;
         };
         skipLines: number;
-        metaChar: string;
+        metaChar: string | null;
         columnNumbers: {
             ref: number;
             start: number;
@@ -40,7 +32,7 @@ export default class CSI extends IndexFile {
     };
     _parse(opts?: Options): Promise<{
         csi: boolean;
-        refCount: any;
+        refCount: number;
         maxBlockSize: number;
         firstDataLine: VirtualOffset | undefined;
         csiVersion: number;
@@ -59,6 +51,42 @@ export default class CSI extends IndexFile {
         refNameToId: {
             [key: string]: number;
         };
+        skipLines: number;
+        metaChar: string | null;
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        format: string;
+        coordinateType: string;
+    } | {
+        csi: boolean;
+        refCount: number;
+        maxBlockSize: number;
+        firstDataLine: VirtualOffset | undefined;
+        csiVersion: number;
+        indices: {
+            binIndex: {
+                [key: string]: Chunk[];
+            };
+            stats: {
+                lineCount: number;
+            } | undefined;
+        }[];
+        depth: number;
+        maxBinNumber: number;
+        maxRefLength: number;
+        refIdToName: never[];
+        refNameToId: {};
+        metaChar: null;
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        coordinateType: string;
+        format: string;
     }>;
     parsePseudoBin(bytes: Buffer, offset: number): {
         lineCount: number;

package/dist/csi.js

@@ -77,16 +77,9 @@ class CSI extends indexFile_1.default {
     indexCov() {
         return __awaiter(this, void 0, void 0, function* () {
             throw new Error('CSI indexes do not support indexcov');
-            return [];
         });
     }
-    parseAuxData(bytes, offset, auxLength) {
-        if (auxLength < 30) {
-            return {
-                refIdToName: [],
-                refNameToId: {},
-            };
-        }
+    parseAuxData(bytes, offset) {
         const formatFlags = bytes.readInt32LE(offset);
         const coordinateType = formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed';
         const format = { 0: 'generic', 1: 'SAM', 2: 'VCF' }[formatFlags & 0xf];
@@ -99,10 +92,10 @@ class CSI extends indexFile_1.default {
             end: bytes.readInt32LE(offset + 12),
         };
         const metaValue = bytes.readInt32LE(offset + 16);
-        const metaChar = metaValue ? String.fromCharCode(metaValue) : '';
+        const metaChar = metaValue ? String.fromCharCode(metaValue) : null;
         const skipLines = bytes.readInt32LE(offset + 20);
         const nameSectionLength = bytes.readInt32LE(offset + 24);
-        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.slice(offset + 28, offset + 28 + nameSectionLength));
+        const { refIdToName, refNameToId } = this._parseNameBytes(bytes.subarray(offset + 28, offset + 28 + nameSectionLength));
         return {
             refIdToName,
             refNameToId,
@@ -153,13 +146,16 @@ class CSI extends indexFile_1.default {
             this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
             const maxRefLength = Math.pow(2, (this.minShift + this.depth * 3));
             const auxLength = bytes.readInt32LE(12);
-            let aux = {
-                refIdToName: [],
-                refNameToId: {},
-            };
-            if (auxLength) {
-                aux = this.parseAuxData(bytes, 16, auxLength);
-            }
+            const aux = auxLength && auxLength >= 30
+                ? this.parseAuxData(bytes, 16)
+                : {
+                    refIdToName: [],
+                    refNameToId: {},
+                    metaChar: null,
+                    columnNumbers: { ref: 0, start: 1, end: 2 },
+                    coordinateType: 'zero-based-half-open',
+                    format: 'generic',
+                };
             const refCount = bytes.readInt32LE(16 + auxLength);
             // read the indexes for each reference sequence
             let firstDataLine;
@@ -202,7 +198,7 @@ class CSI extends indexFile_1.default {
         });
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(Array.prototype.slice.call(bytes, offset + 28, offset + 36), true));
+        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.subarray(offset + 28, offset + 36), true));
         return { lineCount };
     }
     blocksForRange(refName, min, max, opts = {}) {

package/dist/csi.js.map

@@ -1 +1 @@
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+{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,gDAAuB;AACvB,2DAA6C;AAE7C,iEAA0D;AAC1D,oDAA2B;AAC3B,iCAAqD;AAErD,4DAAgD;AAEhD,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACpC,MAAM,UAAU,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAEpC,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,SAAA,CAAC,EAAI,IAAI,CAAA,CAAC,CAAA;AACpC,CAAC;AAED,MAAqB,GAAI,SAAQ,mBAAS;IAIxC,YAAY,IAAS;QACnB,KAAK,CAAC,IAAI,CAAC,CAAA;QACX,IAAI,CAAC,YAAY,GAAG,CAAC,CAAA;QACrB,IAAI,CAAC,KAAK,GAAG,CAAC,CAAA;QACd,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAA;IACnB,CAAC;IACK,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;;YACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;YACxC,IAAI,CAAC,SAAS,EAAE;gBACd,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;YAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YACpC,IAAI,CAAC,GAAG,EAAE;gBACR,OAAO,CAAC,CAAC,CAAA;aACV;YACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;YAC1C,IAAI,KAAK,EAAE;gBACT,OAAO,KAAK,CAAC,SAAS,CAAA;aACvB;YACD,OAAO,CAAC,CAAC,CAAA;QACX,CAAC;KAAA;IACK,QAAQ;;YACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,CAAC,CAAA;QACxD,CAAC;KAAA;IAED,YAAY,CAAC,KAAa,EAAE,MAAc;QACxC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QAC7C,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,MAAM,GAAG,EAAE,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QACtE,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;SACpE;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YAClC,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;YACpC,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC;SACpC,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAChD,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,MAAM,GAAG,EAAE,CAAC,CAAA;QAExD,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;QAED,OAAO;YACL,WAAW;YACX,WAAW;YACX,SAAS;YACT,QAAQ;YACR,aAAa;YACb,MAAM;YACN,cAAc;SACf,CAAA;IACH,CAAC;IAED,eAAe,CAAC,UAAkB;QAChC,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,aAAa,GAAG,CAAC,CAAA;QACrB,MAAM,WAAW,GAAG,EAAE,CAAA;QACtB,MAAM,WAAW,GAA8B,EAAE,CAAA;QACjD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC7C,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE;gBAClB,IAAI,aAAa,GAAG,CAAC,EAAE;oBACrB,IAAI,OAAO,GAAG,UAAU,CAAC,QAAQ,CAAC,MAAM,EAAE,aAAa,EAAE,CAAC,CAAC,CAAA;oBAC3D,OAAO,GAAG,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,CAAA;oBACpC,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;oBAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;iBACjC;gBACD,aAAa,GAAG,CAAC,GAAG,CAAC,CAAA;gBACrB,SAAS,IAAI,CAAC,CAAA;aACf;SACF;QACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;IACrC,CAAC;IAED,4BAA4B;IAEtB,MAAM,CAAC,OAAgB,EAAE;;YAC7B,MAAM,KAAK,GAAG,MAAM,IAAA,uBAAK,EAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAC,CAAA;YAE3E,0BAA0B;YAC1B,IAAI,UAAU,CAAA;YACd,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;gBACxC,UAAU,GAAG,CAAC,CAAA;aACf;iBAAM,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,UAAU,EAAE;gBAC/C,UAAU,GAAG,CAAC,CAAA;aACf;iBAAM;gBACL,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;gBACjC,oDAAoD;aACrD;YAED,IAAI,CAAC,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,CAAC,KAAK,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YACjC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;YAC3D,MAAM,YAAY,GAAG,SAAA,CAAC,EAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA,CAAA;YAC1D,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;YACvC,MAAM,GAAG,GACP,SAAS,IAAI,SAAS,IAAI,EAAE;gBAC1B,CAAC,CAAC,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;gBAC9B,CAAC,CAAC;oBACE,WAAW,EAAE,EAAE;oBACf,WAAW,EAAE,EAAE;oBACf,QAAQ,EAAE,IAAI;oBACd,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;oBAC3C,cAAc,EAAE,sBAAsB;oBACtC,MAAM,EAAE,SAAS;iBAClB,CAAA;YACP,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,GAAG,SAAS,CAAC,CAAA;YAElD,+CAA+C;YAC/C,IAAI,aAAwC,CAAA;YAC5C,IAAI,UAAU,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;YACnC,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;gBACnD,oBAAoB;gBACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;gBAC9C,UAAU,IAAI,CAAC,CAAA;gBACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;gBAC/C,IAAI,KAAK,CAAA,CAAC,iDAAiD;gBAC3D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;oBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;oBAC1C,IAAI,GAAG,GAAG,IAAI,CAAC,YAAY,EAAE;wBAC3B,yDAAyD;wBACzD,qCAAqC;wBACrC,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAClD,UAAU,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,GAAG,EAAE,GAAG,EAAE,CAAA;qBAClC;yBAAM;wBACL,MAAM,OAAO,GAAG,IAAA,yBAAS,EAAC,KAAK,EAAE,UAAU,G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package/dist/indexFile.d.ts

@@ -5,28 +5,48 @@ export interface Options {
     [key: string]: unknown;
     signal?: AbortSignal;
 }
+export interface IndexData {
+    refNameToId: {
+        [key: string]: number;
+    };
+    refIdToName: string[];
+    metaChar: string | null;
+    columnNumbers: {
+        ref: number;
+        start: number;
+        end: number;
+    };
+    coordinateType: string;
+    format: string;
+    [key: string]: any;
+}
 export default abstract class IndexFile {
     filehandle: GenericFilehandle;
     renameRefSeq: (arg0: string) => string;
-    private _parseCache;
-    /**
-     * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
-     */
+    private parseP?;
     constructor({ filehandle, renameRefSeqs, }: {
         filehandle: GenericFilehandle;
         renameRefSeqs?: (a: string) => string;
     });
     abstract lineCount(refName: string, args: Options): Promise<number>;
-    protected abstract _parse(opts: Options): Promise<{
+    protected abstract _parse(opts: Options): Promise<IndexData>;
+    getMetadata(opts?: Options): Promise<{
+        [key: string]: any;
         refNameToId: {
             [key: string]: number;
         };
         refIdToName: string[];
+        metaChar: string | null;
+        columnNumbers: {
+            ref: number;
+            start: number;
+            end: number;
+        };
+        coordinateType: string;
+        format: string;
     }>;
-    getMetadata(opts?: Options): Promise<any>;
     abstract blocksForRange(refName: string, start: number, end: number, opts: Options): Promise<Chunk[]>;
     _findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
-    parse(opts?: Options): Promise<any>;
+    parse(opts?: Options): Promise<IndexData>;
     hasRefSeq(seqId: number, opts?: Options): Promise<boolean>;
 }

package/dist/indexFile.js

@@ -19,17 +19,8 @@ var __rest = (this && this.__rest) || function (s, e) {
         }
     return t;
 };
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
-const quick_lru_1 = __importDefault(require("quick-lru"));
 class IndexFile {
-    /**
-     * @param {filehandle} filehandle
-     * @param {function} [renameRefSeqs]
-     */
     constructor({ filehandle, renameRefSeqs = (n) => n, }) {
         this.filehandle = filehandle;
         this.renameRefSeq = renameRefSeqs;
@@ -53,13 +44,13 @@ class IndexFile {
     }
     parse(opts = {}) {
         return __awaiter(this, void 0, void 0, function* () {
-            if (!this._parseCache) {
-                this._parseCache = new abortable_promise_cache_1.default({
-                    cache: new quick_lru_1.default({ maxSize: 1 }),
-                    fill: () => this._parse(opts),
+            if (!this.parseP) {
+                this.parseP = this._parse(opts).catch(e => {
+                    this.parseP = undefined;
+                    throw e;
                 });
             }
-            return this._parseCache.get('index', null, undefined);
+            return this.parseP;
         });
     }
     hasRefSeq(seqId, opts = {}) {

package/dist/indexFile.js.map

@@ -1 +1 @@
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+{"version":3,"file":"indexFile.js","sourceRoot":"","sources":["../src/indexFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;AAoBA,MAA8B,SAAS;IAKrC,YAAY,EACV,UAAU,EACV,aAAa,GAAG,CAAC,CAAS,EAAE,EAAE,CAAC,CAAC,GAIjC;QACC,IAAI,CAAC,UAAU,GAAG,UAAU,CAAA;QAC5B,IAAI,CAAC,YAAY,GAAG,aAAa,CAAA;IACnC,CAAC;IAMY,WAAW,CAAC,OAAgB,EAAE;;YACzC,6DAA6D;YAC7D,MAAM,KAAuB,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,EAA7C,EAAE,OAAO,OAAoC,EAA/B,IAAI,cAAlB,WAAoB,CAAyB,CAAA;YACnD,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IASD,cAAc,CACZ,UAAqC,EACrC,aAA4B;QAE5B,IAAI,UAAU,EAAE;YACd,OAAO,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;gBAC5C,CAAC,CAAC,aAAa;gBACf,CAAC,CAAC,UAAU,CAAA;SACf;aAAM;YACL,OAAO,aAAa,CAAA;SACrB;IACH,CAAC;IAEK,KAAK,CAAC,OAAgB,EAAE;;YAC5B,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE;gBAChB,IAAI,CAAC,MAAM,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE;oBACxC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAA;oBACvB,MAAM,CAAC,CAAA;gBACT,CAAC,CAAC,CAAA;aACH;YACD,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAEK,SAAS,CAAC,KAAa,EAAE,OAAgB,EAAE;;YAC/C,OAAO,CAAC,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAA;QACnE,CAAC;KAAA;CACF;AA3DD,4BA2DC"}