@gmod/tabix 1.5.14 → 1.6.0

package/CHANGELOG.md

@@ -1,11 +1,15 @@
-## [1.5.14](https://github.com/GMOD/tabix-js/compare/v1.5.13...v1.5.14) (2024-07-23)
+# [1.6.0](https://github.com/GMOD/tabix-js/compare/v1.5.15...v1.6.0) (2024-11-30)
 
 
-### Reverts
 
-* Revert "Bump to eslint 9" ([9bd49b1](https://github.com/GMOD/tabix-js/commit/9bd49b1132f632b0e7847d9b95cf3cb08c424360))
+## [1.5.15](https://github.com/GMOD/tabix-js/compare/v1.5.14...v1.5.15) (2024-08-30)
 
+## [1.5.14](https://github.com/GMOD/tabix-js/compare/v1.5.13...v1.5.14) (2024-07-23)
+
+### Reverts
 
+- Revert "Bump to eslint 9"
+  ([9bd49b1](https://github.com/GMOD/tabix-js/commit/9bd49b1132f632b0e7847d9b95cf3cb08c424360))
 
 ## [1.5.13](https://github.com/GMOD/tabix-js/compare/v1.5.12...v1.5.13) (2024-01-09)
 
@@ -13,8 +17,8 @@
 
 ## [1.5.12](https://github.com/GMOD/tabix-js/compare/v1.5.11...v1.5.12) (2024-01-09)
 
-- Add missing abort signal to the @gmod/abortable-promise-cache fetch for tabix chunks
-  (#143)
+- Add missing abort signal to the @gmod/abortable-promise-cache fetch for tabix
+  chunks (#143)
 
 ## [1.5.11](https://github.com/GMOD/tabix-js/compare/v1.5.10...v1.5.11) (2023-07-10)
 

package/README.md

@@ -22,6 +22,15 @@ const { TabixIndexedFile } = require('@gmod/tabix')
 import { TabixIndexedFile } from '@gmod/tabix'
 ```
 
+### Single file bundle
+
+You can use tabix-js without NPM also with the tabix-bundle.js. See the example
+directory for usage with script tag [example/index.html](example/index.html)
+
+```html
+<script src="https://unpkg.com/@gmod/tabix/dist/tabix-bundle.js"></script>
+```
+
 ### TabixIndexedFile constructor
 
 Basic usage of TabixIndexedFile under node.js supplies a path and optionally a
@@ -38,10 +47,10 @@ const tbiIndexed = new TabixIndexedFile({
 
 ```
 
-You can also use CSI indexes. Note also the usage of the renameRefSeqs callback.
-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)
+You can also use CSI indexes. Note also the usage of the `renameRefSeqs`
+callback. 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
@@ -55,9 +64,15 @@ const csiIndexed = new TabixIndexedFile({
 
 #### TabixIndexedFile constructor with remote files
 
-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
+const remoteTbiIndexed = new TabixIndexedFile({
+  url: 'http://yourhost/file.vcf.gz',
+  tbiUrl: 'http://yourhost/file.vcf.gz.tbi', // can also be csiUrl
+})
+```
+
+You can also alternatively supply a filehandle-like object with the
+[generic-filehandle](https://github.com/GMOD/generic-filehandle): example
 
 ```typescript
 // use a remote file or other filehandle, note RemoteFile comes from https://github.com/GMOD/generic-filehandle
@@ -68,9 +83,9 @@ const remoteTbiIndexed = new TabixIndexedFile({
 })
 ```
 
-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
+This works in both the browser and in node.js, but note that in node.js you may
+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
@@ -102,8 +117,8 @@ await tbiIndexed.getLines('ctgA', 200, 300, function (line, fileOffset) {
 After running this, your `lines` array would contain an array of lines from the
 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
+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 = []
@@ -124,8 +139,8 @@ Notes about the returned values of `getLines`:
 - the callback is also called with a `fileOffset` that can be used to uniquely
   identify lines based on their virtual file offset where the line is found in
   the file
-- if getLines is called with an undefined `end` parameter it gets all lines from
-  start going to the end of the contig e.g.
+- 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 = []
@@ -133,32 +148,164 @@ await tbiIndexed.getLines('ctgA', 0, undefined, line=>lines.push(line))`
 console.log(lines)
 ```
 
-### lineCount
+## API (auto-generated)
+
+### TabixIndexedFile
+
+<!-- Generated by documentation.js. Update this documentation by updating the source code. -->
+
+##### Table of Contents
+
+- [constructor](#constructor)
+  - [Parameters](#parameters)
+- [getLines](#getlines)
+  - [Parameters](#parameters-1)
+- [getHeaderBuffer](#getheaderbuffer)
+  - [Parameters](#parameters-2)
+- [getHeader](#getheader)
+  - [Parameters](#parameters-3)
+- [getReferenceSequenceNames](#getreferencesequencenames)
+  - [Parameters](#parameters-4)
+- [checkLine](#checkline)
+  - [Parameters](#parameters-5)
+- [lineCount](#linecount)
+  - [Parameters](#parameters-6)
+- [readChunk](#readchunk)
+  - [Parameters](#parameters-7)
+
+#### constructor
+
+##### Parameters
+
+- `args`
+  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**&#x20;
+
+  - `args.path`
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
+  - `args.filehandle` **filehandle?**&#x20;
+  - `args.url`
+    **[url](https://developer.mozilla.org/docs/Web/API/URL/URL)?**&#x20;
+  - `args.tbiPath`
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
+  - `args.tbiUrl` **tbiUrl?**&#x20;
+  - `args.tbiFilehandle` **filehandle?**&#x20;
+  - `args.csiPath`
+    **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)?**&#x20;
+  - `args.csiUrl` **csiUrl?**&#x20;
+  - `args.csiFilehandle` **filehandle?**&#x20;
+  - `args.yieldTime`
+    **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?**
+    yield to main thread after N milliseconds if reading features is taking a
+    long time to avoid hanging main thread (optional, default `500`)
+  - `args.renameRefSeqs`
+    **[function](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Statements/function)?**
+    optional function with sig `string => string` to transform reference
+    sequence names for the purpose of indexing and querying. note that the data
+    that is returned is not altered, just the names of the reference sequences
+    that are used for querying. (optional, default `n=>n`)
+  - `args.chunkCacheSize` (optional, default `5*2**20`)
+
+#### getLines
+
+##### Parameters
+
+- `refName`
+  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**
+  name of the reference sequence
+- `s`
+  **([number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
+  |
+  [undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined))**&#x20;
+- `e`
+  **([number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)
+  |
+  [undefined](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/undefined))**&#x20;
+- `opts` **(GetLinesOpts | GetLinesCallback)** callback called for each line in
+  the region. can also pass a object param containing obj.lineCallback,
+  obj.signal, etc
+- `start` start of the region (in 0-based half-open coordinates)
+- `end` end of the region (in 0-based half-open coordinates)
+
+Returns **any** promise that is resolved when the whole read is finished,
+rejected on error
 
-```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 })
-```
+#### getHeaderBuffer
 
-### getHeader
+get a buffer containing the "header" region of the file, which are the bytes up
+to the first non-meta line
 
-```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()
-// or const headerText = await tbiIndexed.getHeader({ signal: aborter.signal })
-```
+##### Parameters
 
-#### getHeaderBuffer
+- `opts` **Options** (optional, default `{}`)
 
-```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 })
-```
+#### getHeader
+
+get a string containing the "header" region of the file, is the portion up to
+the first non-meta line
+
+##### Parameters
+
+- `opts` **Options** (optional, default `{}`)
+
+Returns
+**[Promise](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Promise)**
+for a string
+
+#### getReferenceSequenceNames
+
+get an array of reference sequence names, in the order in which they occur in
+the file. reference sequence renaming is not applied to these names.
+
+##### Parameters
+
+- `opts` **Options** (optional, default `{}`)
+
+#### checkLine
+
+##### Parameters
+
+- `metadata`
+  **[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+  metadata object from the parsed index, containing columnNumbers, metaChar, and
+  format
+- `regionRefName`
+  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**&#x20;
+- `regionStart`
+  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+  region start coordinate (0-based-half-open)
+- `regionEnd`
+  **[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)**
+  region end coordinate (0-based-half-open)
+- `line`
+  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**&#x20;
+
+Returns
+**[object](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object)**
+like `{startCoordinate, overlaps}`. overlaps is boolean, true if line is a data
+line that overlaps the given region
+
+#### lineCount
+
+return the approximate number of data lines in the given reference sequence
+
+##### Parameters
+
+- `refName`
+  **[string](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/String)**&#x20;
+- `opts` **Options** (optional, default `{}`)
+- `refSeq` reference sequence name
+
+Returns **any** number of data lines present on that reference sequence
+
+#### readChunk
+
+read and uncompress the data in a chunk (composed of one or more contiguous
+bgzip blocks) of the file
+
+##### Parameters
+
+- `c` **Chunk**&#x20;
+- `opts` **Options** (optional, default `{}`)
 
 ## Academic Use
 

package/dist/chunk.js

@@ -9,7 +9,6 @@ class Chunk {
         this._fetchedSize = fetchedSize;
     }
     toUniqueString() {
-        // eslint-disable-next-line @typescript-eslint/restrict-template-expressions
         return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
     }
     toString() {

package/dist/chunk.js.map

@@ -1 +1 @@
-{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,4EAA4E;QAC5E,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AA3CD,wBA2CC"}
+{"version":3,"file":"chunk.js","sourceRoot":"","sources":["../src/chunk.ts"],"names":[],"mappings":";;AAEA,iDAAiD;AACjD,MAAqB,KAAK;IAMxB,YACE,IAAmB,EACnB,IAAmB,EACnB,GAAW,EACX,WAAW,GAAG,SAAS;QAEvB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,IAAI,GAAG,IAAI,CAAA;QAChB,IAAI,CAAC,GAAG,GAAG,GAAG,CAAA;QACd,IAAI,CAAC,YAAY,GAAG,WAAW,CAAA;IACjC,CAAC;IAED,cAAc;QACZ,OAAO,GAAG,IAAI,CAAC,IAAI,KAAK,IAAI,CAAC,IAAI,SAC/B,IAAI,CAAC,GACP,iBAAiB,IAAI,CAAC,WAAW,EAAE,GAAG,CAAA;IACxC,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,cAAc,EAAE,CAAA;IAC9B,CAAC;IAED,SAAS,CAAC,CAAQ;QAChB,OAAO,CACL,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,CAAC,IAAI,CAAC;YAC3B,IAAI,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CACjB,CAAA;IACH,CAAC;IAED,WAAW;QACT,IAAI,IAAI,CAAC,YAAY,KAAK,SAAS,EAAE,CAAC;YACpC,OAAO,IAAI,CAAC,YAAY,CAAA;QAC1B,CAAC;QACD,OAAO,IAAI,CAAC,IAAI,CAAC,aAAa,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,aAAa,CAAA;IACtE,CAAC;CACF;AA1CD,wBA0CC"}

package/dist/csi.d.ts

@@ -85,5 +85,5 @@ export default class CSI extends IndexFile {
     /**
      * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
      */
-    reg2bins(beg: number, end: number): number[][];
+    reg2bins(beg: number, end: number): (readonly [number, number])[];
 }

package/dist/csi.js

@@ -15,22 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
@@ -44,10 +45,10 @@ const indexFile_1 = __importDefault(require("./indexFile"));
 const CSI1_MAGIC = 21582659; // CSI\1
 const CSI2_MAGIC = 38359875; // CSI\2
 function lshift(num, bits) {
-    return num * Math.pow(2, bits);
+    return num * 2 ** bits;
 }
 function rshift(num, bits) {
-    return Math.floor(num / Math.pow(2, bits));
+    return Math.floor(num / 2 ** bits);
 }
 class CSI extends indexFile_1.default {
     constructor(args) {
@@ -56,23 +57,21 @@ class CSI extends indexFile_1.default {
         this.depth = 0;
         this.minShift = 0;
     }
-    lineCount(refName_1) {
-        return __awaiter(this, arguments, void 0, function* (refName, opts = {}) {
-            const indexData = yield this.parse(opts);
-            if (!indexData) {
-                return -1;
-            }
-            const refId = indexData.refNameToId[refName];
-            const idx = indexData.indices[refId];
-            if (!idx) {
-                return -1;
-            }
-            const { stats } = indexData.indices[refId];
-            if (stats) {
-                return stats.lineCount;
-            }
+    async lineCount(refName, opts = {}) {
+        const indexData = await this.parse(opts);
+        const refId = indexData.refNameToId[refName];
+        if (refId === undefined) {
             return -1;
-        });
+        }
+        const idx = indexData.indices[refId];
+        if (!idx) {
+            return -1;
+        }
+        const { stats } = indexData.indices[refId];
+        if (stats) {
+            return stats.lineCount;
+        }
+        return -1;
     }
     indexCov() {
         throw new Error('CSI indexes do not support indexcov');
@@ -124,110 +123,115 @@ class CSI extends indexFile_1.default {
         return { refNameToId, refIdToName };
     }
     // fetch and parse the index
-    _parse() {
-        return __awaiter(this, arguments, void 0, function* (opts = {}) {
-            const bytes = yield (0, bgzf_filehandle_1.unzip)(yield this.filehandle.readFile(opts));
-            // check TBI magic numbers
-            let csiVersion;
-            if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
-                csiVersion = 1;
-            }
-            else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
-                csiVersion = 2;
-            }
-            else {
-                throw new Error('Not a CSI file');
-                // TODO: do we need to support big-endian CSI files?
-            }
-            this.minShift = bytes.readInt32LE(4);
-            this.depth = bytes.readInt32LE(8);
-            this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
-            const maxRefLength = Math.pow(2, (this.minShift + this.depth * 3));
-            const auxLength = bytes.readInt32LE(12);
-            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;
-            let currOffset = 16 + auxLength + 4;
-            const indices = new Array(refCount).fill(0).map(() => {
-                // the binning index
-                const binCount = bytes.readInt32LE(currOffset);
-                currOffset += 4;
-                const binIndex = {};
-                let stats; // < provided by parsing a pseudo-bin, if present
-                for (let j = 0; j < binCount; j += 1) {
-                    const bin = bytes.readUInt32LE(currOffset);
-                    if (bin > this.maxBinNumber) {
-                        // this is a fake bin that actually has stats information
-                        // about the reference sequence in it
-                        stats = this.parsePseudoBin(bytes, currOffset + 4);
-                        currOffset += 4 + 8 + 4 + 16 + 16;
-                    }
-                    else {
-                        const loffset = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 4);
-                        firstDataLine = this._findFirstData(firstDataLine, loffset);
-                        const chunkCount = bytes.readInt32LE(currOffset + 12);
+    async _parse(opts = {}) {
+        const bytes = await (0, bgzf_filehandle_1.unzip)(await this.filehandle.readFile(opts));
+        // check TBI magic numbers
+        let csiVersion;
+        if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
+            csiVersion = 1;
+        }
+        else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
+            csiVersion = 2;
+        }
+        else {
+            throw new Error('Not a CSI file');
+            // TODO: do we need to support big-endian CSI files?
+        }
+        this.minShift = bytes.readInt32LE(4);
+        this.depth = bytes.readInt32LE(8);
+        this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7;
+        const maxRefLength = 2 ** (this.minShift + this.depth * 3);
+        const auxLength = bytes.readInt32LE(12);
+        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;
+        let currOffset = 16 + auxLength + 4;
+        const indices = new Array(refCount).fill(0).map(() => {
+            // the binning index
+            const binCount = bytes.readInt32LE(currOffset);
+            currOffset += 4;
+            const binIndex = {};
+            let stats; // < provided by parsing a pseudo-bin, if present
+            for (let j = 0; j < binCount; j += 1) {
+                const bin = bytes.readUInt32LE(currOffset);
+                if (bin > this.maxBinNumber) {
+                    // this is a fake bin that actually has stats information
+                    // about the reference sequence in it
+                    stats = this.parsePseudoBin(bytes, currOffset + 4);
+                    currOffset += 4 + 8 + 4 + 16 + 16;
+                }
+                else {
+                    const loffset = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 4);
+                    firstDataLine = this._findFirstData(firstDataLine, loffset);
+                    const chunkCount = bytes.readInt32LE(currOffset + 12);
+                    currOffset += 16;
+                    const chunks = new Array(chunkCount);
+                    for (let k = 0; k < chunkCount; k += 1) {
+                        const u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
+                        const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
                         currOffset += 16;
-                        const chunks = new Array(chunkCount);
-                        for (let k = 0; k < chunkCount; k += 1) {
-                            const u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                            const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
-                            currOffset += 16;
-                            // this._findFirstData(data, u)
-                            chunks[k] = new chunk_1.default(u, v, bin);
-                        }
-                        binIndex[bin] = chunks;
+                        // this._findFirstData(data, u)
+                        chunks[k] = new chunk_1.default(u, v, bin);
                     }
+                    binIndex[bin] = chunks;
                 }
-                return { binIndex, stats };
-            });
-            return Object.assign(Object.assign({}, aux), { csi: true, refCount, maxBlockSize: 1 << 16, firstDataLine,
-                csiVersion,
-                indices, depth: this.depth, maxBinNumber: this.maxBinNumber, maxRefLength });
+            }
+            return { binIndex, stats };
         });
+        return {
+            ...aux,
+            csi: true,
+            refCount,
+            maxBlockSize: 1 << 16,
+            firstDataLine,
+            csiVersion,
+            indices,
+            depth: this.depth,
+            maxBinNumber: this.maxBinNumber,
+            maxRefLength,
+        };
     }
     parsePseudoBin(bytes, offset) {
         const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 28, offset + 36), true));
         return { lineCount };
     }
-    blocksForRange(refName_1, min_1, max_1) {
-        return __awaiter(this, arguments, void 0, function* (refName, min, max, opts = {}) {
-            if (min < 0) {
-                min = 0;
-            }
-            const indexData = yield this.parse(opts);
-            if (!indexData) {
-                return [];
-            }
-            const refId = indexData.refNameToId[refName];
-            const ba = indexData.indices[refId];
-            if (!ba) {
-                return [];
-            }
-            // const { linearIndex, binIndex } = indexes
-            const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
-            const chunks = [];
-            // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
-            for (const [start, end] of overlappingBins) {
-                for (let bin = start; bin <= end; bin++) {
-                    if (ba.binIndex[bin]) {
-                        for (const c of ba.binIndex[bin]) {
-                            chunks.push(new chunk_1.default(c.minv, c.maxv, bin));
-                        }
+    async blocksForRange(refName, min, max, opts = {}) {
+        if (min < 0) {
+            min = 0;
+        }
+        const indexData = await this.parse(opts);
+        const refId = indexData.refNameToId[refName];
+        if (refId === undefined) {
+            return [];
+        }
+        const ba = indexData.indices[refId];
+        if (!ba) {
+            return [];
+        }
+        // const { linearIndex, binIndex } = indexes
+        const overlappingBins = this.reg2bins(min, max); // List of bin #s that overlap min, max
+        const chunks = [];
+        // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+        for (const [start, end] of overlappingBins) {
+            for (let bin = start; bin <= end; bin++) {
+                if (ba.binIndex[bin]) {
+                    for (const c of ba.binIndex[bin]) {
+                        chunks.push(new chunk_1.default(c.minv, c.maxv, bin));
                     }
                 }
             }
-            return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.default(0, 0));
-        });
+        }
+        return (0, util_1.optimizeChunks)(chunks, new virtualOffset_1.default(0, 0));
     }
     /**
      * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
@@ -237,8 +241,8 @@ class CSI extends indexFile_1.default {
         if (beg < 1) {
             beg = 1;
         }
-        if (end > Math.pow(2, 50)) {
-            end = Math.pow(2, 34);
+        if (end > 2 ** 50) {
+            end = 2 ** 34;
         } // 17 GiB ought to be enough for anybody
         end -= 1;
         let l = 0;