@gmod/tabix 1.5.7 → 1.5.8

package/CHANGELOG.md

@@ -1,6 +1,10 @@
-## [1.5.7](https://github.com/GMOD/tabix-js/compare/v1.5.6...v1.5.7) (2023-03-24)
+## [1.5.8](https://github.com/GMOD/tabix-js/compare/v1.5.7...v1.5.8) (2023-03-24)
+
 
 
+- Make yieldTime optional
+
+## [1.5.7](https://github.com/GMOD/tabix-js/compare/v1.5.6...v1.5.7) (2023-03-24)
 
 - Add yieldTime parameter
 - Improve typescripting

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/tabixIndexedFile.d.ts

@@ -35,7 +35,7 @@ export default class TabixIndexedFile {
         tbiFilehandle?: GenericFilehandle;
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
-        yieldTime: number;
+        yieldTime?: number;
         chunkSizeLimit?: number;
         renameRefSeqs?: (n: string) => string;
         chunkCacheSize?: number;

package/esm/tabixIndexedFile.d.ts

@@ -35,7 +35,7 @@ export default class TabixIndexedFile {
         tbiFilehandle?: GenericFilehandle;
         csiPath?: string;
         csiFilehandle?: GenericFilehandle;
-        yieldTime: number;
+        yieldTime?: number;
         chunkSizeLimit?: number;
         renameRefSeqs?: (n: string) => string;
         chunkCacheSize?: number;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.7",
+  "version": "1.5.8",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",

package/src/tabixIndexedFile.ts

@@ -68,7 +68,7 @@ export default class TabixIndexedFile {
     tbiFilehandle?: GenericFilehandle
     csiPath?: string
     csiFilehandle?: GenericFilehandle
-    yieldTime: number
+    yieldTime?: number
     chunkSizeLimit?: number
     renameRefSeqs?: (n: string) => string
     chunkCacheSize?: number