Merge pull request #464 from akmorrow13/otherGA4GH

Added Variants and Features GA4GH, with GA4GH example file

README.md

@@ -1,5 +1,5 @@
 [![Build Status](https://travis-ci.org/hammerlab/pileup.js.svg?branch=travis-flow)](https://travis-ci.org/hammerlab/pileup.js) [![Coverage Status](https://coveralls.io/repos/hammerlab/pileup.js/badge.svg?branch=master)](https://coveralls.io/r/hammerlab/pileup.js?branch=master) [![NPM version](http://img.shields.io/npm/v/pileup.svg)](https://www.npmjs.org/package/pileup) [![Dependency Status](https://david-dm.org/hammerlab/pileup.js.svg?theme=shields.io)](https://david-dm.org/hammerlab/pileup.js) [![devDependency Status](https://david-dm.org/hammerlab/pileup.js/dev-status.svg?theme=shields.io)](https://david-dm.org/hammerlab/pileup.js#info=devDependencies) [![DOI](https://zenodo.org/badge/8220/hammerlab/pileup.js.svg)](https://zenodo.org/badge/latestdoi/8220/hammerlab/pileup.js)
- [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/hammerlab/pileup.js?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) 
+ [![Gitter](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/hammerlab/pileup.js?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 
 # pileup.js
 pileup.js is an interactive in-browser track viewer. [**Try a demo**][demo]!
@@ -98,6 +98,8 @@ To play with the demo, start an [http-server][hs]:
 
 Then open [http://localhost:8080/examples/index.html](http://localhost:8080/examples/index.html) in your browser of choice.
 
+To view integration with GA4GH schemas, view [http://localhost:8080/examples/ga4gh-example.html](http://localhost:8080/examples/ga4gh-example.html).
+
 ## Testing
 
 Run the tests from the command line:

examples/data-ga4gh.js

@@ -0,0 +1,94 @@
+// Some data for the demo.
+
+// We are going to use the same data source for multiple tracks
+var bamSource = pileup.formats.bam({
+  url: '/test-data/synth3.normal.17.7500000-7515000.bam',
+  indexUrl: '/test-data/synth3.normal.17.7500000-7515000.bam.bai'
+});
+
+// This URL points to the GA4GH Reference Server, which
+// can be accessed for examples of standardized endpoints
+// for genomic data. All available GA4GH endpoints can
+// be found here: http://1kgenomes.ga4gh.org
+var ga4ghReferenceServer = 'http://1kgenomes.ga4gh.org';
+
+var sources = [
+  {
+    viz: pileup.viz.genome(),
+    isReference: true,
+    data: pileup.formats.twoBit({
+      url: 'http://www.biodalliance.org/datasets/hg19.2bit'
+    }),
+    name: 'Reference'
+  },
+  {
+    viz: pileup.viz.scale(),
+    name: 'Scale'
+  },
+  {
+    viz: pileup.viz.location(),
+    name: 'Location'
+  },
+  {
+    viz: pileup.viz.genes(),
+    data: pileup.formats.bigBed({
+      url: 'http://www.biodalliance.org/datasets/ensGene.bb'
+    }),
+    name: 'Genes'
+  },
+  {
+    viz: pileup.viz.variants(),
+    data: pileup.formats.GAVariant({
+        endpoint: ga4ghReferenceServer,
+        variantSetId: "WyIxa2dlbm9tZXMiLCJ2cyIsInBoYXNlMy1yZWxlYXNlIl0",
+        callSetIds: ["WyIxa2dlbm9tZXMiLCJ2cyIsInBoYXNlMy1yZWxlYXNlIiwiSEcwMDA5NiJd"],
+        killChr: true
+    }),
+    options: {
+      onVariantClicked: function(data) {
+        var content = "Variants:\n";
+        for (var i =0;i< data.length;i++) {
+          content += `${data[i].id}: Ref: ${data[i].ref}, Alt: `;
+          data[i].alt.forEach(alt => {
+            content += `${alt} `;
+          })
+          content += '\n';
+        }
+        alert(content);
+      },
+    },
+    name: 'Phase3 Release Variants'
+  },
+  {
+    viz: pileup.viz.features(),
+    data: pileup.formats.GAFeature({
+      endpoint: ga4ghReferenceServer,
+      featureSetId: "WyIxa2dlbm9tZXMiLCJnZW5jb2RlX3YyNGxpZnQzNyJd",
+    }),
+    name: 'gencode_v24lift37'
+  },
+  {
+    viz: pileup.viz.coverage(),
+    data: pileup.formats.GAReadAlignment({
+      endpoint: ga4ghReferenceServer,
+      readGroupId: "WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTEyODc4IiwiU1JSNjIyNDYxIl0",
+      killChr: true,
+      forcedReferenceId: "WyJOQ0JJMzciLCIxIl0"
+    }),
+    cssClass: 'normal',
+    name: 'Coverage'
+  },
+  {
+    viz: pileup.viz.pileup(),
+    data: pileup.formats.GAReadAlignment({
+      endpoint: ga4ghReferenceServer,
+      readGroupId: "WyIxa2dlbm9tZXMiLCJyZ3MiLCJOQTEyODc4IiwiU1JSNjIyNDYxIl0",
+      killChr: true,
+      forcedReferenceId: "WyJOQ0JJMzciLCIxIl0"
+    }),
+    cssClass: 'normal',
+    name: 'NA12878'
+  }
+];
+
+var range = {contig: 'chr1', start: 120000, stop: 125000};

examples/ga4gh-example.html

@@ -0,0 +1,20 @@
+<!doctype html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
+<link rel="stylesheet" href="../style/pileup.css" />
+<link rel="stylesheet" href="demo.css" />
+</head>
+
+<body>
+<button id="jiggle">FPS test</button>
+<div id="pileup"></div>
+</body>
+
+<script src="../node_modules/stats.js/build/stats.min.js"></script>
+<script src="../dist/pileup.js"></script>
+<!-- or:
+<script src="../dist/pileup.min.js"></script>
+-->
+
+<script src="data-ga4gh.js"></script>
+<script src="playground.js"></script>

src/main/ContigInterval.js

@@ -113,6 +113,11 @@ class ContigInterval<T: (number|string)> {
     };
   }
 
+  round(size: number, zeroBased: boolean): ContigInterval<T> {
+    var newInterval = this.interval.round(size, zeroBased);
+    return new ContigInterval(this.contig, newInterval.start, newInterval.stop);
+  }
+
   // Comparator for use with Array.prototype.sort
   static compare(a: ContigInterval, b: ContigInterval): number {
     if (a.contig > b.contig) {

src/main/GA4GHAlignment.js

@@ -39,12 +39,13 @@ class GA4GHAlignment /* implements Alignment */ {
   // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl
   constructor(alignment: Object) {
     this.alignment = alignment;
-    this.pos = alignment.alignment.position.position;
+    this.pos = parseInt(alignment.alignment.position.position);
     this.ref = alignment.alignment.position.referenceName;
     this.name = alignment.fragmentName;
 
     this.cigarOps = alignment.alignment.cigar.map(
-        ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length }));
+        ({operation, operationLength: length}) => ({ op: OP_MAP[operation], length: parseInt(length)})
+    );
     this._interval = new ContigInterval(this.ref,
                                         this.pos,
                                         this.pos + this.getReferenceLength() - 1);
@@ -101,7 +102,7 @@ class GA4GHAlignment /* implements Alignment */ {
     }
   }
 
-  // This is exposed as a static method to facilitate an optimization in GA4GHDataSource.
+  // This is exposed as a static method to facilitate an optimization in GA4GHAlignmentSource.
   static keyFromGA4GHResponse(alignment: Object): string {
     // this.alignment.id would be appealing here, but it's not actually unique!
     return alignment.fragmentName + ':' + alignment.readNumber;

src/main/Interval.js

@@ -39,6 +39,18 @@ class Interval {
     return this.contains(other.start) && this.contains(other.stop);
   }
 
+  // Rounds the interval to the nearest multiples of size.
+  // Optional minimum parameter determines the lowest
+  // possible value for the start of the resulting Interval.
+  round(size: number, zeroBased: boolean): Interval {
+    var minimum = zeroBased ? 0 : 1;
+    var roundDown = x => x - x % size;
+    var newStart = Math.max(minimum, roundDown(this.start)),
+        newStop = roundDown(this.stop + size - 1);
+
+    return new Interval(newStart, newStop);
+  }
+
   clone(): Interval {
     return new Interval(this.start, this.stop);
   }

src/main/RemoteRequest.js

@@ -9,6 +9,8 @@
 import Q from 'q';
 import ContigInterval from './ContigInterval';
 
+var MONSTER_REQUEST = 5000000;
+
 class RemoteRequest {
   url: string;
   cache: Object;
@@ -85,4 +87,7 @@ class RemoteRequest {
   }
 }
 
-module.exports = RemoteRequest;
+module.exports = {
+  RemoteRequest,
+  MONSTER_REQUEST: MONSTER_REQUEST
+};

src/main/data/feature.js

@@ -0,0 +1,43 @@
+/**
+ * Class for parsing features.
+ * @flow
+ */
+'use strict';
+
+import ContigInterval from '../ContigInterval';
+
+class Feature {
+  id: string;
+  featureType: string;
+  contig: string;
+  start: number;
+  stop: number;
+  score: number;
+
+  constructor(feature: Object) {
+   this.id = feature.id;
+   this.featureType = feature.featureType;
+   this.contig = feature.contig;
+   this.start = feature.start;
+   this.stop = feature.stop;
+   this.score = feature.score;
+  }
+
+  static fromGA4GH(ga4ghFeature: Object): Feature {
+   return new Feature(
+     {
+      id: ga4ghFeature.id,
+      featureType: ga4ghFeature.featureType,
+      contig: ga4ghFeature.referenceName,
+      start: ga4ghFeature.start,
+      stop: ga4ghFeature.end,
+      score: 1000
+    });
+  }
+
+  intersects(range: ContigInterval<string>): boolean {
+    return range.intersects(new ContigInterval(this.contig, this.start, this.stop));
+  }
+}
+
+module.exports = Feature;

src/main/data/variant.js

@@ -0,0 +1,62 @@
+/**
+ * Class for parsing variants.
+ * @flow
+ */
+'use strict';
+
+import ContigInterval from '../ContigInterval';
+
+class Variant {
+  contig: string;
+  position: number;
+  ref: string;
+  alt: string;
+  id: string;
+  //this is the biggest allele frequency for single vcf entry
+  //single vcf entry might contain more than one variant like the example below
+  //20 1110696 rs6040355 A G,T 67 PASS NS=2;DP=10;AF=0.333,0.667;AA=T;DB
+  majorFrequency: ?number;
+  //this is the smallest allel frequency for single vcf entry
+  minorFrequency: ?number;
+  vcfLine: string;
+
+
+  constructor(variant: Object) {
+   this.contig = variant.contig;
+   this.position = variant.position;
+   this.ref = variant.ref;
+   this.alt = variant.alt;
+   this.id = variant.id;
+   this.majorFrequency = variant.majorFrequency;
+   this.minorFrequency = variant.minorFrequency;
+   this.vcfLine = variant.vcfLine;
+  }
+
+  static fromGA4GH(ga4ghVariant: Object): Variant {
+   return new Variant(
+    {
+     contig: ga4ghVariant.referenceName,
+     position: ga4ghVariant.start,
+     id: ga4ghVariant.id,
+     ref: ga4ghVariant.referenceBases,
+     alt: ga4ghVariant.alternateBases,
+     majorFrequency: 0,
+     minorFrequency: 0, // TODO extract these
+     vcfLine: "" // TODO
+   });
+  }
+
+  intersects(range: ContigInterval<string>): boolean {
+    return intersects(this, range);
+  }
+
+}
+
+function intersects(variant: Variant, range: ContigInterval<string>): boolean {
+  return range.intersects(new ContigInterval(variant.contig, variant.position, variant.position + 1));
+}
+
+module.exports = {
+  Variant,
+  intersects
+};