open-index/open-npm huggingface dataset:
npm package: @gmmorris/bs-aws-sdk
Description: BuckleScript bindings to the AWS SDK
Author: Gidi Morris
Latest version: 0.1.0

# bs-aws-sdkexpress

AWS SDK bindings for [BuckleScript](https://github.com/bloomberg/bucklescript) in [Reason](https://github.com/facebook/reason).

## Getting Started
Install bs-aws-sdk using npm:
```
npm install --save bs-aws-sdk
```
Then add bs-aws-sdk as a dependency to `bsconfig.json`

Right now the library is at early stages, pull requests are welcome.

### Run the example and tests:

Build and start the server:
```
npm start
```
Run the tests:
```
npm test
```
npm package: @gmo-media/eslint-config
Description: eslint config for gmo-media.
Author: GMO Media,Inc.
Latest version: 2.0.1

# eslint-config

eslint config for gmo-media.

## Basic Usage

Install

```bash
$ npm install --save-dev eslint @gmo-media/eslint-config
```

`.eslintrc`

```json
{
  "extends": "@gmo-media/eslint-config",
  "env": {
    "browser": true
  },
  "rules": {
    "indent": ["error", 2]
  }
}
```

## Rule sets

### `@gmo-media/eslint-config/legacy`
* for legacy JavaScript.

### `@gmo-media/eslint-config/es5`
* for modern es5 script. (default)

### `@gmo-media/eslint-config/es6`
* for es6 script.

### `@gmo-media/eslint-config/react`
* for React.
* Please install the `eslint-plugin-react`.

## Development
1. Edit the rules.
2. `npm test`
3. `npm version XXX -m 'message'`
4. `git push origin master`
5. `git push origin v1.x.x`
6. `npm publish --access=public`

## License

MIT
npm package: @gmo-media/sasslib
Description: Sass libraries for gmo-media
Author: GMO Media,Inc.
Latest version: 3.1.0

# Frontend.sasslib
社内共通のSassライブラリです。

## Install
```bash
$ npm install --save-dev @gmo-media/sasslib
```

## How to use
必要なファイルを import します。

[node-sass-package-importer](https://www.npmjs.com/package/node-sass-package-importer) を使い、

```scss
@import "~@gmo-media/sasslib";
```

とすると `src/` 以下の `utility/` 以外のファイルが全て読み込まれます。

`utility/` 以下のファイルは必要に応じて１つ１つ読み込んでください。

```scss
@import "~@gmo-media/sasslib/src/utility/fix-ios";
```

## Development
```bash
$ git clone git@github.com:gmo-media/Frontend.sasslib.git
$ npm install
```

ファイルを追加修正したら

```bash
$ npm test
```

機能追加したらレビュー依頼してください。

- 必要最低限の要素しか定義しないこと
- 各ファイルは単独で`@import`されても動くこと
- 引数やデフォルト値について十分に検討すること
- `@content`を使って拡張しやすいようにすること

npmに公開するときは、Organizationメンバーのアカウントで

```bash
$ npm run update:minor
```

バグフィックスなどの場合は

```bash
$ npm run update:patch
```
npm package: @gmo-media/stylelint-config
Description: stylelint config for gmo-media.
Author: GMO Media,Inc.
Latest version: 2.1.2

# stylelint-config

stylelint config for gmo-media.

## Basic Usage

Install

```bash
$ npm install --save-dev stylelint @gmo-media/stylelint-config
```

`.stylelintrc`

```json
{
  "extends": "@gmo-media/stylelint-config",
  "rules": {
    "indentation": 4
  }
}
```

Please set the indentation. (default: 4)

## Rule sets

### `@gmo-media/stylelint-config/regular`
* Regular configuration. (default)

### `@gmo-media/stylelint-config/loose`
* Loose configuration.

### `@gmo-media/stylelint-config/extra`
* Extra configuration.

## Development
1. Edit the rules.
2. `npm test`
3. `git commit`
4. `npm version XXX`
5. `git push origin master`
6. `git push origin v1.x.x`
7. `npm publish --access=public`

## License

MIT
npm package: @gmod-workshop/steamdown
Description: Convert Markdown to Steam BBCode
Author: dhkatz
Latest version: 1.1.1

# steamdown

[![Test](https://github.com/gmod-workshop/steamdown/actions/workflows/test.yml/badge.svg)](https://github.com/gmod-workshop/steamdown/actions/workflows/test.yml)
![NPM Version](https://img.shields.io/npm/v/%40gmod-workshop%2Fsteamdown)

Convert Markdown to Steam BBCode.

## Installation

```bash
npm install @gmod-workshop/steamdown
```

## Usage

```typescript
import { Converter } from '@gmod-workshop/steamdown';

const converter = new Converter();
const bbcode = await converter.convert('paragraph');
```


## Features

**Supported Markdown Syntax**

- Paragraph
- Heading
- Blockquote
- List (ordered and unordered)
- Table
- Code
- Horizontal Rule
- Emphasis
- Strong
- Link
- Image
- Strikethrough

**Partially Supported Markdown Syntax**

- Codespan
  - Inline code is not supported by Steam BBCode. 
  - Rendereded as quoted text.
  - Example: \`codespan\` -> 'codespan'
- HTML
  - HTML is not supported by Steam BBCode. Rendereded as is.
- Checkbox
  - Rendereded as a emoji checkbox.
  - Example:
    - `- [x] item` -> '✅ item'
    - `- [ ] item` -> '⬜ item'

**Unsupported Markdown Syntax**

- Autolink
- Footnote
- Definition List
- Abbreviation
- Footnote

## Reference

The following references were used to create this library. If you believe any of the information is incorrect, please open an issue.

- [Steam BBCode](https://steamcommunity.com/sharedfiles/filedetails/?id=2807121939)
npm package: @gmod/abortable-promise-cache
Description: add AbortController support to a cache of async requests
Author: Robert Buels
Latest version: 3.0.4

# @gmod/abortable-promise-cache

[![NPM version](https://img.shields.io/npm/v/@gmod/abortable-promise-cache.svg?style=flat-square)](https://npmjs.org/package/abortable-promise-cache)
[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/abortable-promise-cache/push.yml?branch=master)](https://github.com/GMOD/abortable-promise-cache/actions)

Adds AbortController/AbortSignal semantics to a cache of promises. Each `get`
from the cache can optionally take an `AbortSignal` object that lets that
request be aborted.

Cached fill requests will be aborted and evicted from the cache if all the
incoming requests for it are aborted before the promise settles.

If the fill request has already settled before all the requests for it have been
aborted, it will stay in the cache.

## Install

    $ npm install --save @gmod/abortable-promise-cache

## Usage

```js
import AbortablePromiseCache from '@gmod/abortable-promise-cache'
import QuickLRU from 'quick-lru'

const cache = new AbortablePromiseCache({
  // QuickLRU is a good backing cache to use, but you can use any
  // cache as long as it supports `get`, `set`, `delete`, and `keys`.
  cache: new QuickLRU({ maxSize: 1000 }),

  // the `fill` callback will be called for a cache miss
  async fill(requestData, abortSignal) {
    // do some long-running thing
    return longRunningThing(requestData, abortSignal)
  },
})

// Make a cached request. The returned promise will abort with the given abort signal if
// there is not already a cached copy that has been resolved.
// Fill requests will be signaled to abort if all the requests for them
// so far have been aborted.
const aborter = new AbortController()
const result = await cache.get('some key', { ...anyStuff }, aborter.signal)

// deleting and clearing will abort any outstanding requests
cache.delete('some key')
cache.clear()
```

## API

<!-- Generated by documentation.js. Update this documentation by updating the source code. -->

### Table of Contents

## Academic Use

This package was written with funding from the [NHGRI](http://genome.gov) as
part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
project that you publish, please cite the most recent JBrowse paper, which will
be linked from [jbrowse.org](http://jbrowse.org).

## License

MIT © [Robert Buels](https://github.com/rbuels)
npm package: @gmod/bgzf-filehandle
Description: read from a compressed bgzip file (with .gzi) as if it were uncompressed
Latest version: 6.0.18

[![NPM version](https://img.shields.io/npm/v/@gmod/bgzf-filehandle.svg?style=flat-square)](https://npmjs.org/package/@gmod/bgzf-filehandle)
[![Coverage Status](https://img.shields.io/codecov/c/github/GMOD/bgzf-filehandle/master.svg?style=flat-square)](https://codecov.io/gh/GMOD/bgzf-filehandle/branch/master)
[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/bgzf-filehandle/push.yml?branch=master)](https://github.com/GMOD/bgzf-filehandle/actions)

Transparently read
[indexed block-gzipped (BGZF)](http://www.htslib.org/doc/bgzip.html) files, such
as those created by bgzip, using coordinates from the uncompressed file. The
module is used in @gmod/indexedfasta to read bgzip-indexed fasta files (with gzi
index, fai index, and fa).

Uses WASM (libdeflate) for decompression.

## Install

    $ npm install --save @gmod/bgzf-filehandle

## Usage

### BgzfFilehandle

Read from a bgzip-compressed file with a `.gzi` index as if it were
uncompressed:

```typescript
import { BgzfFilehandle } from '@gmod/bgzf-filehandle'
import { LocalFile } from 'generic-filehandle2'

const f = new BgzfFilehandle({
  filehandle: new LocalFile('path/to/my_file.gz'),
  gziFilehandle: new LocalFile('path/to/my_file.gz.gzi'),
})

const data = await f.read(300, 0) // read(length, position) => Uint8Array
```

### unzip

Decompress an entire BGZF-compressed buffer. Also handles plain gzip:

```typescript
import { unzip } from '@gmod/bgzf-filehandle'

const decompressed = await unzip(compressedData)
```

### unzipChunkSlice

Decompress a range of BGZF blocks and slice out a virtual file offset range
(used by BAM/tabix readers with BAI/TBI indices):

```typescript
import { unzipChunkSlice } from '@gmod/bgzf-filehandle'

const { buffer, cpositions, dpositions } = await unzipChunkSlice(
  compressedData,
  chunk, // { minv: { blockPosition, dataPosition }, maxv: { blockPosition, dataPosition } }
)
```

The returned `cpositions` and `dpositions` give the block boundaries in
compressed and decompressed coordinates, which can be used for generating stable
feature IDs across chunk boundaries.

## Academic Use

This package was written with funding from the [NHGRI](http://genome.gov) as
part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
project that you publish, please cite the most recent JBrowse paper, which will
be linked from [jbrowse.org](http://jbrowse.org).

## License

MIT © [Robert Buels](https://github.com/rbuels)
npm package: @gmod/binary-parser
Description: Blazing-fast binary parser builder
Author: Colin Diesh
Latest version: 1.4.2


# binary-parser

[![Greenkeeper badge](https://badges.greenkeeper.io/GMOD/binary-parser.svg)](https://greenkeeper.io/)
[![Build Status](https://travis-ci.com/GMOD/binary-parser.svg?branch=master)](https://travis-ci.com/GMOD/binary-parser)
[![codecov](https://codecov.io/gh/GMOD/binary-parser/branch/master/graph/badge.svg)](https://codecov.io/gh/GMOD/binary-parser)


@gmod/binary-parser is a fork of https://github.com/keichi/binary-parser that also handles 64-bit longs and itf8 and ltf8 types

## Installation

Binary-parser can be installed with [npm](https://npmjs.org/):

```shell
$ npm install @gmod/binary-parser
```

## Special data types

The ITF-8 and LTF-8 types documented in https://samtools.github.io/hts-specs/CRAMv3.pdf

The 64-bit parsing in this library is done by https://www.npmjs.com/package/long and simply returns .toNumber() on the parsed 64 bit data.

You can also access `Long` inside formatter callbacks (this is not possible in keichi/binary-parser since these are eval'd and the `Long` library instance is not available to the eval'd code)

## Differences with keichi/binary-parser


* This library is default little endian instead instead of big endian while https://github.com/keichi/binary-parser is default big endian

* The return value of the parse `{result: {<parsed results>},offset: <number of bytes parsed>}` instead of just `{<parsed results>}`


## Example usage

Example of reading a 64-bit int

    new Parser()
    .uint64('mylong64bitint')
    .int64('mylong64bitint')

64 bit infers from the endianess of the .endianess, doesn't use uint64le/be

Verification of whether the long is a valid 2^53 int is not done for 64 bit numbers. If you require this make a custom callback using `Long` in a formatter for buffer
npm package: @gmod/faidx
Description: create indexed fasta files
Author: Colin Diesh
Latest version: 2.0.0

[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/faidx-js/push.yml?branch=main&logo=github&style=for-the-badge)](https://github.com/GMOD/faidx-js/actions?query=branch%3Amaster+workflow%3APush+)

## Install

    $ npm install --save @gmod/faidx

## Usage

Operates on a readStream/writeStream

```js
import { generateFastaIndex } from "@gmod/faidx";
const write = fs.createWriteStream("out.fa.fai");
const read = fs.createReadStream("out.fa");
await generateFastaIndex(write, read);
```

## Academic Use

This package was written with funding from the [NHGRI](http://genome.gov) as
part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
project that you publish, please cite the most recent JBrowse paper, which will
be linked from [jbrowse.org](http://jbrowse.org).

## License

MIT © [Colin Diesh](https://github.com/cmdcolin)
npm package: @gmod/genomefeaturecomponent
Description: Provides SVG View for Genome Features rendered with the Apollo Track Web Service from JBrowse data React Component
Latest version: 0.1.4
Deprecated: Please you genomefeaturecomponent instead

# GenomeFeatureComponent

[![Travis][build-badge]][build]
[![npm package][npm-badge]][npm]
[![Coveralls][coveralls-badge]][coveralls]

Describe GenomeFeatureComponent here.

[build-badge]: https://img.shields.io/travis/GMOD/GenomeFeatureComponent/master.png?style=flat-square
[build]: https://travis-ci.org/GMOD/GenomeFeatureComponent

[npm-badge]: https://img.shields.io/npm/v/@gmod/genomefeaturecomponent.png?style=flat-square
[npm]: https://www.npmjs.com/package/@gmod/genomefeaturecomponent

[coveralls-badge]: https://img.shields.io/coveralls/GMOD/GenomeFeatureComponent/master.png?style=flat-square
[coveralls]: https://coveralls.io/github/GMOD/GenomeFeatureComponent


Instructions
============

Make sure you have node 8 or better)

    npm install

    npm start
    
    
View at [http://localhost:3000](http://localhost:3000).


Works by accessing data from an [Apollo server](https://github.com/gmod/apollo).

E.g., http://someserver.org/apollo/track/Honeybee/Official%20Gene%20Set%20v3.2/Group1.1/GB42168-RA.json



```
[{"strand":1,"children":[[{"phase":0,"strand":1,"fmin":329332,"type":"CDS","fmax":329459},{"phase":2,"strand":1,"fmin":329849,"type":"CDS","fmax":330082},{"phase":0,"strand":1,"fmin":330165,"type":"CDS","fmax":330301},{"phase":2,"strand":1,"fmin":330375,"type":"CDS","fmax":330416},{"strand":1,"fmin":329332,"type":"exon","fmax":329459},{"strand":1,"fmin":329849,"type":"exon","fmax":330082},{"strand":1,"fmin":330165,"type":"exon","fmax":330301},{"strand":1,"fmin":330375,"type":"exon","fmax":330416}]],"name":"GB42168-RA","id":"http://demo.genomearchitect.org/Apollo2/track/Honeybee/Official Gene Set v3.2/Group1.1/GB42168-RA.json","fmin":329332,"type":"mRNA","fmax":330416,"selected":true}]
```
npm package: @gmod/http-range-fetcher
Description: caching, aggregating fetch manager for doing lots of HTTP range requests
Author: Robert Buels
Latest version: 5.0.7

# @gmod/http-range-fetcher

[![NPM version](https://img.shields.io/npm/v/@gmod/http-range-fetcher.svg?style=flat-square)](https://npmjs.org/package/@gmod/http-range-fetcher)
[![Build Status](https://img.shields.io/github/actions/workflow/status/rbuels/http-range-fetcher/push.yml?branch=master)](https://github.com/rbuels/http-range-fetcher/actions?query=branch%3Amaster+workflow%3APush+)

Cache/manager for HTTP byte-range requests that merges requests together and
caches results. Designed for applications that request lots of small byte ranges
over HTTP that are often adjacent to each other.

Works both in node or webpack/browserify. Respects HTTP caching semantics, with
the exception of setting a default minimum TTL of 1 second on requests that are
not really supposed to be cached (e.g. `Cache-Control: no-cache`). You can turn
that behavior off by setting `minimumTTL` to 0 though.

## Install

    $ npm install --save http-range-fetcher

## Usage

```js
const { HttpRangeFetcher } = require('http-range-fetcher')

const cache = new HttpRangeFetcher({})
cache.getRange('http://foo.bar/baz.bam', 20, 10).then(response => {
  assert(response.buffer.length === 10)
  assert(response.headers['content-range'] === '20-29/23422')
  // response objects contain `headers` and `buffer`.  the `headers` object
  // contains the original headers that came from the server in response to the
  // aggregated call, except the Content-Range header has been overwritten
  // to match the requested range, and it adds a X-Resource-Length header that
  // conveniently gives the total length of the remote resource so you don't
  // have to parse the Content-Range header.
  assert(response.headers['x-resource-length'] === '23422')
})

// these will be aggregated behind the scenes
// as a single request for a big chunk of the remote file,
// which will be cached to satisfy subsequent requests
Promise.all([
  cache.getRange('http://foo.bar/baz.bam', 20, 10),
  cache.getRange('http://foo.bar/baz.bam', 30, 10),
  cache.getRange('http://foo.bar/baz.bam', 40, 10),
  cache.getRange('http://foo.bar/baz.bam', 50, 10),
  cache.getRange('http://foo.bar/baz.bam', 60, 10),
  cache.getRange('http://foo.bar/baz.bam', 70, 10),
]).then(fetchResults => {
  fetchResults.forEach(res => assert(res.buffer.length === 10))
})
```

<!-- Generated by documentation.js. Update this documentation by updating the source code. -->

### Table of Contents

## Academic Use

This package was written with funding from the [NHGRI](http://genome.gov) as
part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
project that you publish, please cite the most recent JBrowse paper, which will
be linked from [jbrowse.org](http://jbrowse.org).

## License

MIT © [Robert Buels](https://github.com/rbuels)

## Note

Renamed http-range-fetcher -> @gmod/http-range-fetcher in 2024
npm package: @gmod/indexedfasta
Description: read indexed fasta and bgzipped fasta formats
Author: Colin Diesh
Latest version: 5.0.4

[![NPM version](https://img.shields.io/npm/v/@gmod/indexedfasta.svg?style=flat-square)](https://npmjs.org/package/@gmod/indexedfasta)
[![Build Status](https://img.shields.io/github/actions/workflow/status/GMOD/indexedfasta-js/push.yml?branch=main)](https://github.com/GMOD/indexedfasta-js/actions)

## Install

    $ npm install --save @gmod/indexedfasta

## Usage

```typescript
import { IndexedFasta, BgzipIndexedFasta } from '@gmod/indexedfasta'

const t = new IndexedFasta({
  path: 'test.fa',
  faiPath: 'test.fa.fai',
})
// or
const t = new BgzipIndexedFasta({
  path: 'test.fa.gz',
  faiPath: 'test.fa.gz.fai',
  gziPath: 'test.fa.gz.gzi',
})

// get the first 10 bases of a sequence from the file.
// coordinates are UCSC standard 0-based half-open
//
const chr1Region = await t.getSequence('chr1', 0, 10)
// chr1Region is now a string of bases, 'ACTG...'

// get a whole sequence from the file
const chr1Bases = await t.getSequence('chr1')

// get object with all seq lengths as { seqName => length, ... }
const allSequenceSizes = await t.getSequenceSizes()

// get the size of a single sequence
const chr1Size = await t.getSequenceSize('chr1')

// get an array of all sequence names in the file
const seqNames = await t.getSequenceNames()
```

If you are using in the browser, you may use the generic-filehandle2 package and
initialize like this

```typescript
import { IndexedFasta, BgzipIndexedFasta } from '@gmod/indexedfasta'
import { RemoteFile } from 'generic-filehandle2'

const t = new IndexedFasta({
  fasta: new RemoteFile('http://yoursite.com/test.fa'),
  fai: new RemoteFile('http://yoursite.com/test.fa.fai'),
})
const t = new BgzipIndexedFasta({
  fasta: new RemoteFile('http://yoursite.com/test.fa.gz'),
  fai: new RemoteFile('http://yoursite.com/test.fa.gz.fai'),
  gzi: new RemoteFile('http://yoursite.com/test.fa.gz.gzi'),
})
```

In node.js you can also access remote files with generic-filehandle2, but you
would supply a fetch function e.g.

```typescript
import { IndexedFasta, BgzipIndexedFasta } from '@gmod/indexedfasta'
import { RemoteFile } from 'generic-filehandle2'
import fetch from 'cross-fetch'

const t = new IndexedFasta({
  fasta: new RemoteFile('http://yoursite.com/test.fa', { fetch }),
  fai: new RemoteFile('http://yoursite.com/test.fa.fai', { fetch }),
})
```

## Academic Use

This package was written with funding from the [NHGRI](http://genome.gov) as
part of the [JBrowse](http://jbrowse.org) project. If you use it in an academic
project that you publish, please cite the most recent JBrowse paper, which will
be linked from [jbrowse.org](http://jbrowse.org).

## License

MIT © [Colin Diesh](https://github.com/cmdcolin)
npm package: @gmod/jbrowse-web
Description: This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
Latest version: 0.0.1-beta.25

This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).

## Available Scripts

In the project directory, you can run:

### `npm start`

Runs the app in the development mode.<br>
Open [http://localhost:3000](http://localhost:3000) to view it in the browser.

The page will reload if you make edits.<br>
You will also see any lint errors in the console.

### `npm test`

Launches the test runner in the interactive watch mode.<br>
See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.

### `npm run build`

Builds the app for production to the `build` folder.<br>
It correctly bundles React in production mode and optimizes the build for the best performance.

The build is minified and the filenames include the hashes.<br>
Your app is ready to be deployed!

See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.

### `npm run eject`

**Note: this is a one-way operation. Once you `eject`, you can’t go back!**

If you aren’t satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.

Instead, it will copy all the configuration files and the transitive dependencies (Webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you’re on your own.

You don’t have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn’t feel obligated to use this feature. However we understand that this tool wouldn’t be useful if you couldn’t customize it when you are ready for it.

## Learn More

You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).

To learn React, check out the [React documentation](https://reactjs.org/).