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Robinson"},"license":"MIT","homepage":"https://igv.org","keywords":["IGV","genomics","visualization","bioinformatics"],"repository":{"type":"git","url":"git+https://github.com/igvteam/igv.js.git"},"description":"Embeddable genomic visualization component based on the Integrative Genomics Viewer","contributors":[{"name":"Douglass Turner"}],"maintainers":[{"name":"feifei9606","email":"1360599809@qq.com"}],"readme":"# igv.js\r\n![build](https://github.com/igvteam/igv.js/actions/workflows/ci_build.yml/badge.svg)\r\n[![](https://img.shields.io/npm/dw/igv.svg)](https://www.npmjs.com/package/igv)\r\n[![](https://img.shields.io/github/last-commit/igvteam/igv.js.svg)](https://github.com/igvteam/igv.js)\r\n[![](https://img.shields.io/npm/l/igv.svg)](LICENSE)\r\n[![](https://data.jsdelivr.com/v1/package/npm/igv/badge)](https://www.jsdelivr.com/package/npm/igv)\r\n\r\nigv.js is an embeddable interactive genome visualization component developed by the \r\n [Integrative Genomics Viewer (IGV)](https://igv.org) team. \r\n\r\n## Citing igv.js\r\n\r\nJames T Robinson, Helga Thorvaldsdottir, Douglass Turner, Jill P Mesirov, igv.js: an embeddable JavaScript \r\nimplementation of the Integrative Genomics Viewer (IGV), Bioinformatics, Volume 39, Issue 1, January 2023, \r\nbtac830, https://doi.org/10.1093/bioinformatics/btac830\r\n \r\nBelow are examples and a quickstart guide.  See the [developer documentation](https://igv.org/doc/igvjs) for more documentation.  \r\n\r\n# Examples\r\n \r\n***[Alignments](https://igv.org/web/release/3.0.8/examples/cram-vcf.html)***\r\n\r\n***[Interactions](https://igv.org/web/release/3.0.8/examples/interact.html)***\r\n\r\n***[Copy number](https://igv.org/web/release/3.0.8/examples/copyNumber.html)***\r\n\r\n***[Multiple regions](https://igv.org/web/release/3.0.8/examples/multi-locus.html)***\r\n\r\n***[Mutation Annotation Format (MAF)](https://igv.org/web/release/3.0.8/examples/maf-tcga.html)***\r\n\r\n***[Variant color options](https://igv.org/web/release/3.0.8/examples/variant-colors.html)***\r\n\r\n***[More](https://igv.org/web/release/3.0.8/examples/)***\r\n\r\n \r\n# Quickstart\r\n\r\n## Installation\r\nigv.js consists of a single javascript file with no external dependencies.  \r\n\r\nPre-built files for script include, AMD, or CJS module systems (igv.min.js) and an ES6 module (igv.esm.min.js)\r\ncan be downloaded from [https://cdn.jsdelivr.net/npm/igv@3.0.8/dist/](https://cdn.jsdelivr.net/npm/igv@3.0.8/dist/). \r\n\r\nTo import igv as an ES6 module\r\n\r\n```javascript\r\nimport igv from \"https://cdn.jsdelivr.net/npm/igv@3.0.8/dist/igv.esm.min.js\"\r\n``` \r\n\r\nOr as a script include (defines the \"igv\" global)\r\n\r\n```html\r\n<script src=\"https://cdn.jsdelivr.net/npm/igv@3.0.8/dist/igv.min.js\"></script>\r\n```   \r\n \r\nAlternatively you can install with npm  \r\n \r\n ```npm install igv```\r\n\r\nand source the appropriate file for your module system (igv.min.js or igv.esm.min.js)  in node_modules/igv/dist.\r\n\r\n\r\n## Usage\r\n\r\nTo create an igv.js ***browser*** supply a container div \r\nand an initial configuration defining the reference genome, initial tracks, and other state to the \r\nfunction ```igv.createBrowser(div, config)```.  \r\n\r\nThis function returns a promise for an igv.Browser object which can used to control the browser.  For example, to open\r\na browser on a single alignment track opened at a specific locus:\r\n\r\n```\r\n      var igvDiv = document.getElementById(\"igv-div\");\r\n      var options =\r\n        {\r\n            genome: \"hg38\",\r\n            locus: \"chr8:127,736,588-127,739,371\",\r\n            tracks: [\r\n                {\r\n                    \"name\": \"HG00103\",\r\n                    \"url\": \"https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram\",\r\n                    \"indexURL\": \"https://s3.amazonaws.com/1000genomes/data/HG00103/alignment/HG00103.alt_bwamem_GRCh38DH.20150718.GBR.low_coverage.cram.crai\",\r\n                    \"format\": \"cram\"\r\n                }\r\n            ]\r\n        };\r\n\r\n        igv.createBrowser(igvDiv, options)\r\n                .then(function (browser) {\r\n                    console.log(\"Created IGV browser\");\r\n                })\r\n```\r\n\r\n## Documentation\r\n\r\nFull documentation of the igv.js API is available at [https://igv.org/doc/igvjs/](https://igv.org/doc/igvjs/).\r\n\r\n## Development\r\n\r\n### Requirements\r\n\r\nBuilding igv.js and running the examples require Linux or MacOS.  Other Unix environments will probably\r\nwork but have not been tested.  \r\n\r\nWindows users can use [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10).\r\n\r\n### Building\r\n\r\nBuilding igv.js and running the examples requires [node.js](https://nodejs.org/).\r\n\r\n\r\n```  \r\ngit clone https://github.com/igvteam/igv.js.git\r\ncd igv.js\r\nnpm install\r\nnpm run build\r\n```\r\n\r\nThis creates a dist folder with the following files\r\n\r\n* igv.js - UMDS file for script include, AMD, or CJS modules.  A script include will define an \"igv\" global.\r\n* igv.min.js - minified version of igv.js\r\n* igv.esm.js --  ES6 module \r\n* igv.esm.min.js --  minified version of igv.esm.js\r\n\r\n### Tests\r\n\r\nTo run the tests from the command line\r\n\r\n```\r\nnpm run test\r\n```\r\n\r\n\r\n### Examples\r\n\r\nTo run the examples install [http-server](https://www.npmjs.com/package/http-server).\r\n\r\nStart  http-server from the project root directory\r\n\r\n```bash\r\nnpx http-server \r\n```\r\n\r\nThen open [http://localhost:8080/examples](http://localhost:8080/examples) in a web browser.\r\n\r\n\r\n# Supported Browsers\r\n\r\nigv.js require a modern web browser with support for Javascript ECMAScript 2015 (ES6). \r\n\r\n# License\r\n\r\nigv.js is [MIT](/LICENSE) licensed.\r\n\r\n\r\n\r\n### [Release Notes](https://github.com/igvteam/igv.js/releases)\r\n\r\n \r\n","readmeFilename":"README.md"}