bionode-fastq - npm Package Compare versions

Comparing version 0.1.0 to 2.1.0

index.js

@@ -1,1 +0,1 @@
-module.exports = require('./lib/bionode-fastq')
+module.exports = require('./lib/bionode-fastq')

lib/bionode-fastq.js

@@ -1,46 +0,39 @@
-var fs = require('fs');
-var stream = require('stream');
-var readline = require('readline');
+var fs = require('fs')
+var Stream = require('stream')
+var readline = require('readline')
 
-var block = [];
+var events = require('events')
 
+var block = []
+
 var toObject = function (block) {
+  return {
+    name: block[0],
+    seq: block[1],
+    name2: block[2],
+    qual: block[3]
+  }
+}
 
-    return {
-        name: block[0],
-        seq: block[1],
-        name2: block[2],
-        qual: block[3]
-    }
+var fastq = new events.EventEmitter()
+fastq.read = function (path) {
+  var instream = fs.createReadStream(path)
+  var outstream = new Stream()
+  var rl = readline.createInterface(instream, outstream)
 
-};
-
-var fastq = {
-
-    toFastQ: function (path, onFeature, onEnd) {
-
-        var instream = fs.createReadStream(path);
-        var outstream = new stream();
-        var rl = readline.createInterface(instream, outstream);
-
-        rl.on('line', function (line) {
-            block.push(line);
-
-            if (block.length == 4) {
-                var obj = toObject(block);
-                onFeature(obj);
-                block = [];
-            }
-        });
-
-        rl.on('close', function () {
-            if (onEnd) {
-                onEnd();
-            }
-        });
-
+  rl.on('line', function (line) {
+    block.push(line)
+    if (block.length === 4) {
+      var obj = toObject(block)
+      fastq.emit('data', obj)
+      block = []
     }
+  })
 
-};
+  rl.on('close', function () {
+    fastq.emit('end')
+  })
+  return this
+}
 
-module.exports = fastq;
+module.exports = fastq

package.json

 {
   "name": "bionode-fastq",
-  "version": "0.1.0",
+  "version": "2.1.0",
   "homepage": "http://bionode.io",
   "description": "Streamable FASTQ parser",
   "scripts": {
-    "test": "mocha"
+    "test": "standard && mocha",
+    "coverage": "istanbul cover ./node_modules/mocha/bin/_mocha --report lcovonly -- -R spec",
+    "coveralls": "istanbul cover ./node_modules/mocha/bin/_mocha --report lcovonly -- -R spec && cat ./coverage/lcov.info | ./node_modules/coveralls/bin/coveralls.js && rm -rf ./coverage"
   },
@@ -28,4 +30,7 @@ "author": {
     "chai": "^2.2.0",
-    "mocha": "^2.2.4"
+    "mocha": "^2.2.4",
+    "standard": "^3.5.0",
+    "coveralls": "^2.11.2",
+    "istanbul": "^0.3.13"
   }
 }

README.md

@@ -9,4 +9,32 @@ <p align="center">
 # bionode-fastq
-> Streamable FASTQ parser.    
+> Streamable FASTQ parser.
 
-[![Build Status](https://travis-ci.org/bionode/bionode-fastq.svg?branch=master)](https://travis-ci.org/bionode/bionode-fastq)
+[![NPM][npm-stats-image]][npm-stats-url]
+
+[![NPM version][npm-image]][npm-url]
+[![Build Status][travis-image]][travis-url]
+[![Coveralls Status][coveralls-image]][coveralls-url]
+[![Dependency Status][depstat-image]][depstat-url]
+[![Standard style][js-standard-style-image]][js-standard-style-url]  
+[![Gitter chat][gitter-image]][gitter-url]
+[![DOI][doi-image]][doi-url]  
+[![Stories in Ready at waffle.io][waffle-image]][waffle-url]
+
+[npm-stats-url]: https://nodei.co/npm/bionode-fastq
+[npm-stats-image]: https://nodei.co/npm/bionode-fastq.png?downloads=true&downloadRank=true&stars=true
+[npm-url]: http://npmjs.org/package/bionode-fastq
+[npm-image]: http://img.shields.io/npm/v/bionode-fastq.svg?style=flat-square
+[travis-url]: http://travis-ci.org/bionode/bionode-fastq
+[travis-image]: http://img.shields.io/travis/bionode/bionode-fastq.svg?style=flat-square
+[coveralls-url]: http://coveralls.io/r/bionode/bionode-fastq
+[coveralls-image]: http://img.shields.io/coveralls/bionode/bionode-fastq.svg?style=flat-square
+[depstat-url]: http://david-dm.org/bionode/bionode-fastq
+[depstat-image]: http://img.shields.io/david/bionode/bionode-fastq.svg?style=flat-square
+[js-standard-style-url]: https://github.com/feross/standard
+[js-standard-style-image]: https://img.shields.io/badge/code%20style-standard-brightgreen.svg?style=flat-square
+[gitter-image]: http://img.shields.io/badge/gitter-bionode/bionode--fastq-brightgreen.svg?style=flat-square
+[gitter-url]: https://gitter.im/bionode/bionode-fastq
+[waffle-image]: https://badge.waffle.io/bionode/bionode-fastq.png?label=ready&title=issues%20ready
+[waffle-url]: https://waffle.io/bionode/bionode-fastq
+[doi-url]: http://dx.doi.org/?
+[doi-image]: http://img.shields.io/badge/doi-NA/NA-blue.svg?style=flat-square

test/toFastQ.js

@@ -1,28 +0,28 @@
-'use strict';
-var should = require('chai').should();
-var fastq = require('../index');
+/* global describe, it */
+'use strict'
+require('chai').should()
+var fastq = require('../index')
 
-
 describe('toFastQ', function () {
+  this.timeout(4000)
+  var output = []
 
-    this.timeout(4000);
-    var output = [];
+  it('should run without error', function (done) {
+    var applyToEach = function (item) {
+      output.push(item)
+    }
+    var onEnd = function (err) {
+      if (err) {
+        return done(err)
+      }
+      return done()
+    }
 
-    it('should run without error', function (done) {
-        var applyToEach = function (item) {
-            output.push(item);
-        };
-        var onEnd = function (err) {
-            if (err) {
-                return done(err);
-            }
-            return done();
-        };
-        fastq.toFastQ('test/data/sample.fq', applyToEach, onEnd);
-    });
+    fastq.read('test/data/sample.fq').on('data', applyToEach).on('end', onEnd)
+  })
 
-    it('should process 100 objects', function (done) {
-        output.length.should.equal(100);
-        done();
-    });
-});
+  it('should process 100 objects', function (done) {
+    output.length.should.equal(100)
+    done()
+  })
+})

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

No v1

Quality

Package is not semver >=1. This means it is not stable and does not support ^ ranges.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

17731

increased by13.75%

Lines of code

57

increased by1.79%

Number of low quality alerts

0

decreased by-100%

Number of lines in readme file

40

increased by233.33%

Worsened metrics

Dev dependency count

5

increased by150%

No dependency changes