Merge 441974a into dd04040

.gitignore

@@ -32,6 +32,6 @@ typings
 build
 
 # Genomics
-*.2bit
-*.bb
-*.bed
+/*.2bit
+/*.bb
+/*.bed

Gruntfile.js

@@ -87,20 +87,30 @@ module.exports = function(grunt) {
     },
     mocha_phantomjs: {
       run: {
-        src: ['test/runner.html']
+        options: {
+          urls: ['http://localhost:9501/test/runner.html']
+        }
       },
       cov: {
-        src: ['test/coverage.html'],
         options: {
+          urls: ['http://localhost:9501/test/coverage.html'],
           reporter: 'node_modules/mocha-lcov-reporter/lib/lcov.js',
           output: 'build/bundled.lcov',
           silent: true
         }
       }
+    },
+    connect: {
+      server: {
+        options: {
+          port: 9501
+        }
+      }
     }
   });
 
   grunt.loadNpmTasks('grunt-browserify');
+  grunt.loadNpmTasks('grunt-contrib-connect');
   grunt.loadNpmTasks('grunt-contrib-watch');
   grunt.loadNpmTasks('grunt-flow-type-check');
   grunt.loadNpmTasks('grunt-mocha-phantomjs');
@@ -111,8 +121,8 @@ module.exports = function(grunt) {
   grunt.registerTask('watchFlow', ['flow:app:start', 'watch:flow']);
   grunt.registerTask('prod', ['browserify:dist', 'uglify:dist']);
   grunt.registerTask('browsertests', ['browserify:test']);
-  grunt.registerTask('test', ['browsertests', 'mocha_phantomjs:run']);
+  grunt.registerTask('test', ['browsertests', 'connect', 'mocha_phantomjs:run']);
   grunt.registerTask('travis', ['flow', 'test']);
   grunt.registerTask('coverage',
-                     ['browsertests', 'exorcise:bundle', 'jscoverage', 'mocha_phantomjs:cov']);
+                     ['browsertests', 'exorcise:bundle', 'jscoverage', 'connect', 'mocha_phantomjs:cov']);
 };

package.json

@@ -27,6 +27,7 @@
     "flow-bin": "^0.4.0",
     "grunt": "^0.4.5",
     "grunt-browserify": "^3.3.0",
+    "grunt-contrib-connect": "^0.9.0",
     "grunt-contrib-uglify": "^0.8.0",
     "grunt-contrib-watch": "^0.6.1",
     "grunt-env": "^0.4.2",

src/RemoteFile.js

@@ -49,15 +49,11 @@ class RemoteFile {
     xhr.setRequestHeader('Range', `bytes=${start}-${stop}`);
     var remoteFile = this;
     xhr.onload = function(e) {
+      // The actual length of the response may be less than requested if it's
+      // too short, e.g. if we request bytes 0-1000 of a 500-byte file.
       var buffer = this.response;
-      var expectLength = stop - start + 1,
-          actualLength = buffer.byteLength;
-      if (actualLength != expectLength) {
-        deferred.reject(`Server returned incorrect number of bytes for ${this.url}. Requested ${start}-${stop} (${expectLength} bytes) but received ${actualLength}.`);
-        return;
-      }
 
-      var newChunk = { start, stop, buffer };
+      var newChunk = { start, stop: start + buffer.byteLength - 1, buffer };
       remoteFile.chunks.push(newChunk);
       deferred.resolve(new DataView(buffer));
     };

test/TwoBit-test.js

@@ -0,0 +1,49 @@
+var chai = require('chai');
+var expect = chai.expect;
+var assert = chai.assert;
+
+var TwoBit = require('../src/TwoBit');
+
+describe('TwoBit', function() {
+  function getTestTwoBit() {
+    // This file was generated using UCSC tools:
+    // twoBitToFa -seqList=./test/seqList.txt hg19.2bit /tmp/extract.fa
+    // perl -i -pe 's/:.*//' /tmp/extract.fa
+    // faToTwoBit /tmp/extract.fa test/data/test.2bit
+    return new TwoBit('/test/data/test.2bit');
+  }
+
+  it('should have the right contigs', function(done) {
+    var twoBit = getTestTwoBit();
+    twoBit.getContigList()
+        .then(contigs => {
+          expect(contigs).to.deep.equal(['chr1', 'chr17', 'chr22']);
+          done();
+        })
+        .done();
+  });
+
+  it('should extract unknowns', function(done) {
+    // This test mirrors dalliance's (chr22:19178140-19178170)
+    var twoBit = getTestTwoBit();
+    twoBit.getFeaturesInRange('chr22', 1, 31)
+        .then(basePairs => {
+          expect(basePairs).to.equal('NTCACAGATCACCATACCATNTNNNGNNCNA');
+          done();
+        })
+        .done();
+  });
+
+  it('should reject invalid contigs', function(done) {
+    var twoBit = getTestTwoBit();
+    twoBit.getFeaturesInRange('chrZ')
+          .then(() => { assert.fail('Should have thrown'); })
+          .catch(err => {
+            expect(err).to.match(/Invalid contig/);
+          })
+          .fin(done)
+          .done();
+  });
+
+  // TODO: masked regions
+});

test/seqList.txt

@@ -0,0 +1,3 @@
+chr1:19178000-19178170
+chr17:7512444-7531642
+chr22:19178139-19179170