bionode-vcf - npm Package Compare versions

Comparing version 1.1.5 to 1.3.0

lib/index.js

@@ -9,148 +9,165 @@ /*
 
+var fs = require('fs')
+var readline = require('readline')
+var Stream = require('stream')
+var events = require('events')
+var zlib = require('zlib')
+var unzip = require('unzip-stream')
 
-var fs = require('fs');
-var readline = require('readline');
-var Stream = require('stream');
-var events = require('events');
+var vcf = new events.EventEmitter()
 
-var vcf = new events.EventEmitter();
+function parseStream (instream, extension) {
+  var rl
+  var numSamples = 0
+  var sampleIndex = {}
+  var vcfAttrib = {}
+  var outstream = new Stream()
 
-vcf.read = function (path) {
+  switch (extension) {
+    case 'gz':
+      rl = readline.createInterface({
+        input: instream.pipe(zlib.createGunzip())
+      })
+      break
+    case 'zip':
+      rl = readline.createInterface({
+        input: instream.pipe(unzip.Parse())
+      })
+      break
+    case 'vcf':
+      rl = readline.createInterface(instream, outstream)
+      break
+    default:
+      var err = new Error('File format not supported')
+      vcf.emit('error', err)
+  }
 
-    var instream = fs.createReadStream(path);
-    var outstream = new Stream();
-    var rl = readline.createInterface(instream, outstream);
+  rl.on('line', function (line) {
+    // check if line starts with hash and use them
+    if (line.indexOf('#') === 0) {
+      // ##fileformat=VCFv4.1
+      if (!vcfAttrib.vcf_v) {
+        vcfAttrib.vcf_v = line.match(/^##fileformat=/) ? line.split('=')[1] : null
+      }
 
-    var numSamples = 0;
-    var sampleIndex = {};
-    var vcfAttrib = {};
+      // ##samtoolsVersion=0.1.19-44428cd
+      if (!vcfAttrib.samtools) {
+        vcfAttrib.samtools = line.match(/^##samtoolsVersion=/) ? line.split('=')[1] : null
+      }
 
+      // ##reference=file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa
+      if (!vcfAttrib.refseq) {
+        vcfAttrib.refseq = line.match((/^##reference=file:/)) ? line.split('=')[1] : null
+      }
 
-    rl.on('line', function(line) {
+      // #CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tsample1\tsample2\tsample3
+      // set number of samples in vcf file
+      if (line.match(/^#CHROM/)) {
+        var sampleinfo = line.split('\t')
+        numSamples = sampleinfo.length - 9
 
-        // check if line starts with hash and use them
-        if (line.indexOf('#') == 0) {
+        for (var i = 0; i < numSamples; i++) {
+          sampleIndex[i] = sampleinfo[9 + i]
+        }
+      }
+    } else { // go through remaining lines
+            // split line by tab character
+      var info = line.split('\t')
 
-            //##fileformat=VCFv4.1
-            if (!vcfAttrib.vcf_v) {
-                vcfAttrib.vcf_v = line.match(/^##fileformat=/) ?  line.split('=')[1] : null ;
-            }
+      if (info.length < 9) {
+        var err = new Error('number of columns in the file are less than expected in vcf')
+        vcf.emit('error', err)
+      }
 
-            //##samtoolsVersion=0.1.19-44428cd
-            if (!vcfAttrib.samtools) {
-                vcfAttrib.samtools = line.match(/^##samtoolsVersion=/) ? line.split('=')[1] : null ;
-            }
+      // format information ids
+      var formatIds = info[8].split(':')
 
-            //##reference=file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa
-            if (!vcfAttrib.refseq) {
-                vcfAttrib.refseq = line.match((/^##reference=file:/)) ? line.split('=')[1] : null ;
-            }
+      // parse the sample information
+      var sampleObject = []
+      for (var j = 0; j < numSamples; j++) {
+        var sampleData = {}
+        sampleData['NAME'] = sampleIndex[j]
+        var formatParts = info[9].split(':')
+        for (var k = 0; k < formatParts.length; k++) {
+          sampleData[formatIds[k]] = formatParts[k]
+        }
+        sampleObject.push(sampleData)
+      }
 
-            //#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2	sample3
-            //set number of samples in vcf file
-            if (line.match(/^#CHROM/)) {
-                var sampleinfo = line.split('\t');
-                numSamples = sampleinfo.length - 9;
+      // parse the variant call information
+      var varInfo = info[7].split(';')
+      var infoObject = {}
 
-                for (var i = 0; i < numSamples; i++) {
-                    sampleIndex[i] = sampleinfo[9 + i];
-                }
-
-            }
-
-
+      // check if the variant is INDEL or SNP
+      // and assign the specific type of variation identified
+      var type
+      var typeInfo
+      if (varInfo[0].match(/^INDEL$/)) {
+        type = 'INDEL'
+        varInfo.shift()
+        if (info[3].length > info[4].length) {
+          typeInfo = 'deletion'
+        } else if (info[3].length < info[4].length) {
+          typeInfo = 'insertion'
+        } else if (info[3].length === info[4].length) {
+          typeInfo = 'substitution - multi'
         }
-        // go through remaining lines
-        else {
-            // split line by tab character
-            var info = line.split('\t');
+      } else {
+        type = 'SNP'
+        if (info[3].length === 1) {
+          typeInfo = 'substitution'
+        } else if (info[3].length > 1) {
+          typeInfo = 'substitution - multi'
+        }
+      }
+      infoObject['VAR'] = type
+      infoObject['VARINFO'] = typeInfo
 
-            if (info.length < 9) {
-                var err = new Error('number of columns in the file are less than expected in vcf');
-                vcf.emit('error', err);
-            }
+      // variant info added to object
+      for (var l = 0; l < varInfo.length; l++) {
+        var pair = varInfo[l].split('=')
+        infoObject[pair[0]] = pair[1]
+      }
 
-            // format information ids
-            var formatIds = info[8].split(':');
+      // parse the variant information
+      var varData = {
+        chr: info[0],
+        pos: info[1],
+        id: info[2],
+        ref: info[3],
+        alt: info[4],
+        qual: info[5],
+        filter: info[6],
+        varinfo: infoObject,
+        sampleinfo: sampleObject,
+        attributes: vcfAttrib
+      }
 
-            // parse the sample information
-            var sampleObject = [];
-            for (var j = 0; j < numSamples; j++) {
-                var sampleData = {};
-                sampleData['NAME'] = sampleIndex[j];
-                var formatParts = info[9].split(':');
-                for (var k = 0; k < formatParts.length; k++) {
-                    sampleData[formatIds[k]] = formatParts[k];
-                }
-                sampleObject.push(sampleData)
-            }
+      // console.log('Variant data',varData);
+      vcf.emit('data', varData)
+    }
+  })
 
-            // parse the variant call information
-            var varInfo = info[7].split(';');
-            var infoObject = {};
+  rl.on('close', function () {
+    vcf.emit('end')
+  })
+}
 
-            // check if the variant is INDEL or SNP
-            // and assign the specific type of variation identified
-            var type;
-            var typeInfo;
-            if (varInfo[0].match(/^INDEL$/)) {
-                type = 'INDEL';
-                varInfo.shift();
-                if (info[3].length > info[4].length) {
-                    typeInfo = 'deletion';
-                }
-                else if  (info[3].length < info[4].length) {
-                    typeInfo = 'insertion';
-                }
-                else if  (info[3].length == info[4].length) {
-                    typeInfo = 'substitution - multi';
-                }
-            }
-            else {
-                type = 'SNP';
-                if (info[3].length == 1) {
-                    typeInfo = 'substitution';
-                }
-                else if  (info[3].length > 1) {
-                    typeInfo = 'substitution - multi';
-                }
-            }
-            infoObject['VAR'] = type;
-            infoObject['VARINFO'] = typeInfo;
+// To read file in stream and parse it
+vcf.read = function (path) {
+  var instream = fs.createReadStream(path)
+  var extension = path.split('.').pop()
 
-            // variant info added to object
-            for (var l = 0; l < varInfo.length; l++) {
-                var pair = varInfo[l].split("=");
-                infoObject[pair[0]] = pair[1];
-            }
+  parseStream(instream, extension)
 
-            // parse the variant information
-            var varData = {
-                chr: info[0],
-                pos: info[1],
-                id: info[2],
-                ref: info[3],
-                alt: info[4],
-                qual: info[5],
-                filter: info[6],
-                varinfo: infoObject,
-                sampleinfo: sampleObject,
-                attributes: vcfAttrib
-            };
+  return this
+}
 
-            //console.log('Variant data',varData);
-            vcf.emit('data', varData);
+// To parse stream data sent by user
+vcf.readStream = function (instream, extension = 'vcf') {
+  parseStream(instream, extension)
 
-        }
+  return this
+}
 
-    });
-
-    rl.on('close', function () {
-        vcf.emit('end');
-    });
-
-    return this;
-
-};
-
-module.exports = vcf;
+module.exports = vcf

package.json

 {
   "name": "bionode-vcf",
   "description": "a vcf parser in javascript",
-  "version": "1.1.5",
-  "homepage": "https://github.com/shyamrallapalli/bionode-vcf",
+  "version": "1.3.0",
+  "homepage": "https://github.com/bionode/bionode-vcf",
   "author": {
@@ -12,6 +12,6 @@ "name": "Shyam Rallapalli",
     "type": "git",
-    "url": "git://github.com/shyamrallapalli/bionode-vcf.git"
+    "url": "git://github.com/bionode/bionode-vcf.git"
   },
   "bugs": {
-    "url": "https://github.com/shyamrallapalli/bionode-vcf/issues"
+    "url": "https://github.com/bionode/bionode-vcf/issues"
   },
@@ -21,3 +21,3 @@ "licenses": [
       "type": "MIT",
-      "url": "https://github.com/shyamrallapalli/bionode-vcf/blob/master/LICENSE"
+      "url": "https://github.com/bionode/bionode-vcf/blob/master/LICENSE"
     }
@@ -27,12 +27,15 @@ ],
   "scripts": {
-    "test": "mocha"
+    "test": "standard && dependency-check . && mocha"
   },
   "dependencies": {
-    "events": "^1.1.0",
-    "readline": "^1.2.1",
-    "stream": "0.0.2"
+    "events": "^1.1.1",
+    "readline": "^1.3.0",
+    "stream": "0.0.2",
+    "unzip-stream": "^0.3.0"
   },
   "devDependencies": {
-    "chai": "^3.4.1",
-    "mocha": "^2.3.4"
+    "chai": "^4.0.1",
+    "dependency-check": "^2.8.0",
+    "mocha": "^3.4.2",
+    "standard": "^10.0.2"
   },
@@ -39,0 +42,0 @@ "keywords": [

README.md

@@ -0,20 +1,55 @@
+<p align="center">
+  <a href="http://bionode.io">
+    <img height="200" width="200" title="bionode" alt="bionode logo" src="https://rawgithub.com/bionode/bionode/master/docs/bionode-logo.min.svg"/>
+  </a>
+  <br/>
+  <a href="http://bionode.io/">bionode.io</a>
+</p>
+
+
 # bionode-vcf
 
-[![NPM version](http://img.shields.io/npm/v/bionode-vcf.svg)](https://www.npmjs.org/package/bionode-vcf)
-[![Build Status](https://secure.travis-ci.org/bionode/bionode-vcf.png?branch=master)](http://travis-ci.org/bionode/bionode-vcf)
-
 > a vcf parser in javascript
 
-## Getting Started
+[![npm](https://img.shields.io/npm/v/bionode-vcf.svg?style=flat-square)](http://npmjs.org/package/bionode-vcf)
+[![Travis](https://img.shields.io/travis/bionode/bionode-vcf.svg?style=flat-square)](https://travis-ci.org/bionode/bionode-vcf)
+[![Coveralls](https://img.shields.io/coveralls/bionode/bionode-vcf.svg?style=flat-square)](http://coveralls.io/r/bionode/bionode-vcf)
+[![Dependencies](http://img.shields.io/david/bionode/bionode-vcf.svg?style=flat-square)](http://david-dm.org/bionode/bionode-vcf)
+[![npm](https://img.shields.io/npm/dt/bionode-vcf.svg?style=flat-square)](https://www.npmjs.com/package/bionode-vcf)
+[![Gitter](https://img.shields.io/gitter/room/nwjs/nw.js.svg?style=flat-square)](https://gitter.im/bionode/bionode)
 
-#### installation
 
-Install the module with: 
+## Install
 
+You need to install the latest Node.JS first, please check [nodejs.org](http://nodejs.org) or do the following:
+
 ```bash
-npm install bionode-vcf
+# Ubuntu
+sudo apt-get install npm
+# Mac
+brew install node
+# Both
+npm install -g n
+n stable
 ```
 
-#### usage
+To use `bionode-vcf` as a command line tool, you can install it globally with `-g`.
 
+```bash
+npm install bionode-vcf -g
+```
+
+Or, if you want to use it as a JavaScript library, you need to install it in your local project folder inside the `node_modules` directory by doing the same command **without** `-g`.
+
+```bash
+npm i bionode-vcf # 'i' can be used as shortcut to 'install'
+```
+
+
+### Usage
+
+#### vcf.read
+- `vcf.read` takes params: `path`
+- The supported filetypes are `vcf`, `zip` and `gz`.
+
 ```javascript
@@ -37,40 +72,37 @@ var vcf = require('bionode-vcf');
 
-## Documentation
-VCF format specifications and more information about the fileds can be found at
-[1000 genomes webpage](http://www.1000genomes.org/wiki/analysis/variant%20call%20format/vcf-variant-call-format-version-41) and
-[samtools github page](https://github.com/samtools/hts-specs)
+#### vcf.readStream
+- `vcf.readStream` takes params: `stream` and `extension`
+- The supported extension are `vcf`, `zip` and `gz`.
 
-## Contributing
+```javascript
+var vcf = require('bionode-vcf');
+var fileStream = s3.getObject({
+    Bucket: [BUCKETNAME],
+    Key: [FILENAME]
+}).createReadStream();  // or stream data from any other source
 
-All contributions are welcome.
+vcf.read(filestream, 'zip'); // default value is `vcf`
+vcf.on('data', function(feature){
+    console.log(feature);
+})
 
-## Support
+vcf.on('end', function(){
+    console.log('end of file')
+})
 
-If you have any problem or suggestion please open an issue [here](https://github.com/bionode/bionode-vcf/issues).
+vcf.on('error', function(err){
+    console.error('it\'s not a vcf', err)
+})
 
-## License 
+```
 
-The MIT License
+## Documentation
 
-Copyright (c) 2015, Shyam Rallapalli and Martin Page
+VCF format specifications and more information about the fileds can be found at
+[1000 genomes webpage](http://www.1000genomes.org/wiki/analysis/variant%20call%20format/vcf-variant-call-format-version-41) and
+[samtools github page](https://github.com/samtools/hts-specs)
 
-Permission is hereby granted, free of charge, to any person
-obtaining a copy of this software and associated documentation
-files (the "Software"), to deal in the Software without
-restriction, including without limitation the rights to use,
-copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the
-Software is furnished to do so, subject to the following
-conditions:
 
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
+## Contributing
 
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-OTHER DEALINGS IN THE SOFTWARE.
+We welcome all kinds of contributions at all levels of experience, please read the [CONTRIBUTING.md](CONTRIBUTING.md) to get started!

test/test_vcf.js

@@ -0,1 +1,2 @@
+/* global describe it */
 /*
@@ -10,125 +11,168 @@ * bionode-vcf
 // chai is an assertion library
-//var chai = require('chai');
+// var chai = require('chai');
 
 // @see http://chaijs.com/api/assert/
-//var assert = chai.assert;
+// var assert = chai.assert;
 
 // register alternative styles
 // @see http://chaijs.com/api/bdd/
-//chai.expect();
-//chai.should();
+// chai.expect();
+// chai.should();
 
 // requires your main app (specified in index.js)
-var VCF = require('../lib/index');
-var path = require('path');
-var assert = require('assert');
-var filePath = path.join(__dirname, 'sample.vcf');
+var VCF = require('../lib/index')
+var fs = require('fs')
+var path = require('path')
+var assert = require('assert')
 
-var allFeatures = [];
+var allFeatures = []
 
-describe('VCF', function(){
-  describe('.read', function(){
-    it('should read without error', function(done){
+describe('VCF', function () {
+  describe('.read .vcf file', function () {
+    var filePath = path.join(__dirname, 'sample.vcf')
 
-        function onFeature(vcf) {
-            allFeatures.push(vcf);
-        }
+    it('should read without error', function (finish) {
+      function onFeature (vcf) {
+        allFeatures.push(vcf)
+      }
 
-        VCF.read(filePath).on('data', onFeature).on('end', done);
+      VCF.read(filePath).on('data', onFeature).once('end', finish)
+    })
+    it('should look like a valid output', function () {
+      assert.notStrictEqual(allFeatures, validOutput)
+    })
+  })
 
-    });
+  describe('.read .gz file', function () {
+    var filePath = path.join(__dirname, 'sample.gz')
+
+    it('should read without error', function (done) {
+      function onFeature (vcf) {
+        allFeatures.push(vcf)
+      }
+
+      VCF.read(filePath).on('data', onFeature).once('end', done)
+    })
     it('should look like a valid output', function () {
-        assert.notStrictEqual(allFeatures, validOutput);
+      assert.notStrictEqual(allFeatures, validOutput)
     })
-  });
-});
+  })
 
+  describe('.read .zip file', function () {
+    var filePath = path.join(__dirname, 'sample.zip')
+    it('should read without error', function (done) {
+      function onFeature (vcf) {
+        allFeatures.push(vcf)
+      }
 
+      VCF.read(filePath).on('data', onFeature).once('end', done)
+    })
+    it('should look like a valid output', function () {
+      assert.notStrictEqual(allFeatures, validOutput)
+    })
+  })
+
+  describe('.readStream', function () {
+    var filePath = path.join(__dirname, 'sample.vcf')
+    var fileStream = fs.createReadStream(filePath)
+
+    it('should read without error', function (finish) {
+      function onFeature (vcf) {
+        allFeatures.push(vcf)
+      }
+
+      VCF.readStream(fileStream).on('data', onFeature).once('end', finish)
+    })
+    it('should look like a valid output', function () {
+      assert.notStrictEqual(allFeatures, validOutput)
+    })
+  })
+})
+
 var validOutput = [
-    {   chr: 'Cf746836_TGAC_s1v1_scaffold_4',
-        pos: '5607',
-        id: '.',
-        ref: 'G',
-        alt: 'C',
-        qual: '18.1',
-        filter: '.',
-        varinfo:
-        {   VAR: 'SNP',
-            VARINFO: 'substitution',
-            DP: '6',
-            VDB: '6.560000e-02',
-            RPB: '1.427508e+00',
-            AF1:' 0.5',
-            AC1: '1',
-            DP4: '3,1,1,1',
-            MQ: '60',
-            FQ: '21',
-            PV4: '1,0.0023,1,1' },
-        sampleinfo:
-            [ { NAME: 'foxley_wood1_bwa-mem-sorted.bam',
-                GT: '0/1',
-                PL: '48,0,123',
-                GQ: '51' } ],
-        attributes:
-        {   vcfver: 'VCFv4.1',
-            samtools: '0.1.19-44428cd',
-            reference: 'file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa' }
-    },
-    {   chr: 'Cf746836_TGAC_s1v1_scaffold_12',
-        pos: '672',
-        id: '.',
-        ref: 'CAAA',
-        alt: 'CAA',
-        qual: '128',
-        filter: '.',
-        varinfo:
-        {   VAR: 'INDEL',
-            VARINFO: 'deletion',
-            IS: '16,0.727273',
-            DP: '22',
-            VDB: '1.896486e-01',
-            AF1: '1',
-            AC1: '2',
-            DP4: '0,0,0,20',
-            MQ: '60',
-            FQ: '-94.5' },
-        sampleinfo:
-            [ { NAME: 'foxley_wood1_bwa-mem-sorted.bam',
-                GT: '1/1',
-                PL: '169,60,0',
-                GQ: '99' } ],
-        attributes:
-        {   vcfver: 'VCFv4.1',
-            samtools: '0.1.19-44428cd',
-            reference: 'file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa' }
-    },
-    {   chr: 'Cf746836_TGAC_s1v1_scaffold_12',
-        pos: '2911',
-        id: '.',
-        ref: 'ATA',
-        alt: 'ATACTCGGTA',
-        qual: '214',
-        filter: '.',
-        varinfo:
-        {   VAR: 'INDEL',
-            VARINFO: 'insertion',
-            IS: '16,0.727273',
-            DP: '22',
-            VDB: '3.802706e-02',
-            AF1: '1',
-            AC1: '2',
-            DP4: '0,0,9,8',
-            MQ: '60',
-            FQ: '-85.5' },
-        sampleinfo:
-            [ { NAME: 'foxley_wood1_bwa-mem-sorted.bam',
-                GT: '1/1',
-                PL: '255,51,0',
-                GQ: '99' } ],
-        attributes:
-        {   vcfver: 'VCFv4.1',
-            samtools: '0.1.19-44428cd',
-            reference: 'file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa' }
-    }
-];
-
+  { chr: 'Cf746836_TGAC_s1v1_scaffold_4',
+    pos: '5607',
+    id: '.',
+    ref: 'G',
+    alt: 'C',
+    qual: '18.1',
+    filter: '.',
+    varinfo:
+    { VAR: 'SNP',
+      VARINFO: 'substitution',
+      DP: '6',
+      VDB: '6.560000e-02',
+      RPB: '1.427508e+00',
+      AF1: ' 0.5',
+      AC1: '1',
+      DP4: '3,1,1,1',
+      MQ: '60',
+      FQ: '21',
+      PV4: '1,0.0023,1,1' },
+    sampleinfo:
+    [ { NAME: 'foxley_wood1_bwa-mem-sorted.bam',
+      GT: '0/1',
+      PL: '48,0,123',
+      GQ: '51' } ],
+    attributes:
+    { vcfver: 'VCFv4.1',
+      samtools: '0.1.19-44428cd',
+      reference: 'file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa' }
+  },
+  { chr: 'Cf746836_TGAC_s1v1_scaffold_12',
+    pos: '672',
+    id: '.',
+    ref: 'CAAA',
+    alt: 'CAA',
+    qual: '128',
+    filter: '.',
+    varinfo:
+    { VAR: 'INDEL',
+      VARINFO: 'deletion',
+      IS: '16,0.727273',
+      DP: '22',
+      VDB: '1.896486e-01',
+      AF1: '1',
+      AC1: '2',
+      DP4: '0,0,0,20',
+      MQ: '60',
+      FQ: '-94.5' },
+    sampleinfo:
+    [ { NAME: 'foxley_wood1_bwa-mem-sorted.bam',
+      GT: '1/1',
+      PL: '169,60,0',
+      GQ: '99' } ],
+    attributes:
+    { vcfver: 'VCFv4.1',
+      samtools: '0.1.19-44428cd',
+      reference: 'file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa' }
+  },
+  { chr: 'Cf746836_TGAC_s1v1_scaffold_12',
+    pos: '2911',
+    id: '.',
+    ref: 'ATA',
+    alt: 'ATACTCGGTA',
+    qual: '214',
+    filter: '.',
+    varinfo:
+    { VAR: 'INDEL',
+      VARINFO: 'insertion',
+      IS: '16,0.727273',
+      DP: '22',
+      VDB: '3.802706e-02',
+      AF1: '1',
+      AC1: '2',
+      DP4: '0,0,9,8',
+      MQ: '60',
+      FQ: '-85.5' },
+    sampleinfo:
+    [ { NAME: 'foxley_wood1_bwa-mem-sorted.bam',
+      GT: '1/1',
+      PL: '255,51,0',
+      GQ: '99' } ],
+    attributes:
+    { vcfver: 'VCFv4.1',
+      samtools: '0.1.19-44428cd',
+      reference: 'file://../index/Chalara_fraxinea_TGAC_s1v1_scaffolds.fa' }
+  }
+]

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

Native code

Supply chain risk

Contains native code (e.g., compiled binaries or shared libraries). Including native code can obscure malicious behavior.

Found 1 instance in 1 package

Major refactor

Supply chain risk

Package has recently undergone a major refactor. It may be unstable or indicate significant internal changes. Use caution when updating to versions that include significant changes.

Found 1 instance in 1 package

New author

Supply chain risk

A new npm collaborator published a version of the package for the first time. New collaborators are usually benign additions to a project, but do indicate a change to the security surface area of a package.

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

Improved metrics

Total package byte prevSize

30698

increased by83.37%

Number of package files

12

increased by50%

Lines of code

308

increased by25.71%

Number of lines in readme file

108

increased by42.11%

Worsened metrics

Dependency count

4

increased by33.33%

Dev dependency count

4

increased by100%

Number of low supply chain risk alerts

2

increased by100%

Number of medium supply chain risk alerts

3

increased byInfinity%

Dependency changes

• + Addedunzip-stream@^0.3.0

• + Addedbinary@0.3.0(transitive)

• + Addedbuffers@0.1.1(transitive)

• + Addedchainsaw@0.1.0(transitive)

• + Addedminimist@1.2.8(transitive)

• + Addedmkdirp@0.5.6(transitive)

• + Addedtraverse@0.3.9(transitive)

• + Addedunzip-stream@0.3.4(transitive)

• Updatedevents@^1.1.1

• Updatedreadline@^1.3.0