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Genomediff\n\n![Travis build status](https://travis-ci.org/biosustain/genomediff-node.svg)\n[![Dependency Status](https://gemnasium.com/badges/github.com/biosustain/genomediff-node.svg)](https://gemnasium.com/github.com/biosustain/genomediff-node)\n\n> Parses strings from files in the GenomeDiff format generated by the breseq variant caller for haploid microbial organisms.\n\n### Installation\n----------------\n```shell\n$(node bin)/npm install genomediff\n```\n**Note**: It has only been tested with Node 5.\n\n\n### Usage\n---------\n\n**GenomeDiff** strings are parsed using `GenomeDiff.parse(<string>)`. The **GenomeDiff** object contains a `metadata` dict with the meta data, as well as `mutations`, `evidence` and `validation` lists, each containing records of that type. Records can be accessed through this list or by id using `GenomeDiff.parse(<string>)[<id>]`. **GenomeDiff** is an iterable and iterating it will return all properties and records.\n\nFor accessing all the records you can use `GenomeDiff.parse('<string>').values()` which returns an iterable but only with the `Record` types.\n\nFor accessing the parents of a specific mutation you can use the `parents` property available on each record:\n```js\nlet doc = GenomeDiff.parse('<string>'); // a genomediff string\nlet someMutation = doc[12]; // mutation with id '12'\nsomeMutation.parents // this will lookup all the parents of the record with id `12` and return as an array of Records\n```\n\nIf you want to get an attribute from a parent record then you can use the `.get(<attribute>)` method available on the record to do so:\n```js\nlet doc = GenomeDiff.parse('<string>'); // a genomediff string\nlet someMutation = doc[12]; // mutation with id '12'\nsomeMutation.get('coverage') // this will lookup all the parents of the record with id `12` and return the value of the attribute `coverage` if found on any of the parent records\n```\n\nIf used with node, you can use the following:\n```js\nvar GenomeDiff = require('genomediff').GenomeDiff;\nvar fs = require('fs');\nvar file = fs.readFileSync('<path>', \"utf8\"); // path to your `.gd` file\nvar doc = GenomeDiff.parse(file);\n```\n\nIf used in a browser, use:\n```js\nimport {GenomeDiff} from 'genomediff';\nvar doc = GenomeDiff.parse('<string>'); // a genomediff string\n```\n**Note**: Keep in mind that this package requires an ES6 environment in order to work.\n\n\n### Running Tests\n-----------------\nA full test suite can be run using `npm test`. If you wish to run tests on file change, use `jasmine-node dist/ --autotest --color --verbose`.\n\n### Development\n---------------\nWhen developing, use `tsc --watch` to build the `.ts` files on change. Alternatively, you can use `npm run build` if you do not wish to run the build on file change.\n\n**Note**: If you add new files or remove files, make sure to edit the `\"files\"` field in `tsconfig.json`:\n```js\n\"files\": [\n\t\"./typings/typings.d.ts\", // never remove this line\n\t// add more files after this line\n\t\"./src/parser.ts\",\n\t\"./src/parser.spec.ts\",\n\t\"./src/records.ts\",\n\t\"./src/records.spec.ts\",\n\t\"./src/gd.ts\",\n\t\"./src/gd.spec.ts\"\n]\n```\n","maintainers":[{"email":"lars@lyschoening.de","name":"lyschoening"},{"email":"rolandjitsu@gmail.com","name":"rolandjitsu"}],"time":{"modified":"2022-06-18T07:30:49.441Z","created":"2015-12-01T13:46:33.666Z","1.0.0":"2015-12-01T13:46:33.666Z","1.0.1":"2015-12-02T09:05:32.881Z","1.0.2":"2015-12-02T09:20:16.543Z","1.0.3":"2015-12-02T09:51:57.611Z","1.0.4":"2015-12-02T09:57:36.016Z","1.0.5":"2015-12-02T10:08:31.996Z","1.0.6":"2015-12-02T10:25:23.454Z","1.0.7":"2015-12-02T10:38:44.166Z","1.0.8":"2015-12-07T13:01:59.822Z","1.1.0":"2015-12-07T14:16:07.435Z","1.1.1":"2015-12-08T08:34:05.197Z","1.1.2":"2015-12-08T08:42:34.174Z","1.1.3":"2015-12-08T08:48:11.567Z","1.1.4":"2015-12-08T08:56:37.443Z","1.2.0":"2015-12-08T09:14:58.755Z","1.3.0":"2015-12-08T12:52:30.979Z","1.4.0":"2015-12-08T13:20:40.713Z","1.4.1":"2015-12-10T13:31:08.675Z","1.5.0":"2015-12-16T10:18:24.123Z","1.5.1":"2015-12-16T10:28:45.151Z","1.5.2":"2015-12-16T10:49:17.711Z","1.5.3":"2015-12-16T12:11:19.049Z","1.5.4":"2016-01-08T09:27:07.936Z","1.5.5":"2016-02-17T10:10:27.358Z","1.5.6":"2016-02-17T10:20:37.026Z","1.6.0":"2016-02-17T11:00:15.588Z","1.7.0":"2016-02-17T12:19:20.981Z","1.7.1":"2016-04-19T13:37:42.482Z"},"homepage":"https://github.com/biosustain/genomediff-node#readme","keywords":["genomediff","gd","biology","laboratory","genome","sequencing","parser","biojs"],"repository":{"type":"git","url":"git+https://github.com/biosustain/genomediff-node.git"},"author":{"name":"Roland Groza","email":"rolandjitsu@gmail.com "},"bugs":{"url":"https://github.com/biosustain/genomediff-node/issues"},"license":"MIT","readmeFilename":"README.md"}