add some tests, fix some bugs

src/SamRead.js

@@ -62,10 +62,10 @@ class SamRead {
 
     // Go ahead and parse a few fields immediately.
     var jv = this._getJDataView();
-    this.refID = jv.getUint32(0);
+    this.refID = jv.getInt32(0);
     this.ref = ref;
-    this.pos = jv.getUint32(4);
-    this.l_seq = jv.getUint32(16);
+    this.pos = jv.getInt32(4);
+    this.l_seq = jv.getInt32(16);
   }
 
   toString(): string {

src/TwoBitDataSource.js

@@ -113,7 +113,7 @@ var createTwoBitDataSource = function(remoteSource: TwoBit): TwoBitSource {
   function getRangeAsString(range: GenomeRange): string {
     if (!range) return '';
     return _.range(range.start, range.stop + 1)
-        .map(x => getBasePair(range.contig, x))
+        .map(x => getBasePair(range.contig, x) || '.')
         .join('');
   }
 

src/bam.js

@@ -233,7 +233,13 @@ class Bam {
       var slice = function(u8: Uint8Array) {
         return u8.buffer.slice(u8.byteOffset, u8.byteOffset + u8.byteLength - 1);
       };
-      o.alignments = o.alignments.map(x => new SamRead(slice(x.contents), vo, ''));
+      o.alignments = o.alignments.map(x => {
+        var r = new SamRead(slice(x.contents), vo, '');
+        if (r.refID != -1) {
+          r.ref = o.header.references[r.refID].name;
+        }
+        return r;
+      });
       return o;
     });
   }

test/SamRead-test.js

@@ -2,32 +2,18 @@
 'use strict';
 
 import type * as Q from 'q';
+import type * as SamRead from '../src/SamRead';
 
 var expect = require('chai').expect;
 
-var jBinary = require('jbinary');
-
 var RemoteFile = require('../src/RemoteFile'),
-    utils = require('../src/utils'),
-    bamTypes = require('../src/formats/bamTypes'),
-    SamRead = require('../src/SamRead'),
-    VirtualOffset = require('../src/VirtualOffset'),
+    Bam = require('../src/bam'),
     ContigInterval = require('../src/ContigInterval');
 
 describe('SamRead', function() {
 
   function getSamArray(url): Q.Promise<SamRead[]> {
-    var zero = new VirtualOffset(0, 0);
-    var file = new RemoteFile(url);
-    return file.getAll().then(gzipBuffer => {
-      var buf = utils.inflateGzip(gzipBuffer);
-      var jb = new jBinary(buf, bamTypes.TYPE_SET);
-      jb.read('BamHeader');  // skip past the header to get to alignments.
-      return jb.read(['array', {
-        block_size: 'int32',
-        contents: ['blob', 'block_size']
-      }]).map(block => new SamRead(block.contents, zero, 'ref'));
-    });
+    return new Bam(new RemoteFile(url)).readAll().then(d => d.alignments);
   }
 
   var testReads = getSamArray('/test/data/test_input_1_a.bam');
@@ -46,10 +32,10 @@ describe('SamRead', function() {
       var read = reads[0];
       expect(read.getName()).to.equal('r000');
       expect(read.refID).to.equal(0);
-      expect(read.ref).to.equal('ref');
+      expect(read.ref).to.equal('insert');
       expect(read.pos).to.equal(49);  // 0-based
       expect(read.l_seq).to.equal(10);
-      expect(read.toString()).to.equal('ref:50-59');
+      expect(read.toString()).to.equal('insert:50-59');
       expect(read.getCigarOps()).to.deep.equal([{op: 'M', length: 10}]);
 
       // This one has a more interesting Cigar string
@@ -73,7 +59,7 @@ describe('SamRead', function() {
       var r000 = reads[0].getFull();
       expect(r000.read_name).to.equal('r000');
       expect(r000.FLAG).to.equal(99);
-      expect(r000.refID).to.equal(0);
+      expect(reads[0].ref).to.equal('insert');
       // .. POS
       expect(r000.MAPQ).to.equal(30);
       expect(reads[0].getCigarString()).to.equal('10M');
@@ -88,19 +74,23 @@ describe('SamRead', function() {
       expect(aux).to.have.length(2);
       expect(aux[0]).to.contain({tag: 'RG', value: 'cow'});
       expect(aux[1]).to.contain({tag: 'PG', value: 'bull'});
+
+      expect(reads).to.have.length(15);
+      expect(reads[14].refID).to.equal(-1);  // unmapped read
+      expect(reads[14].ref).to.equal('');
     });
   });
 
   it('should find record intersections', function() {
     return testReads.then(reads => {
       var read = reads[0];
       // toString() produces a 1-based result, but ContigInterval is 0-based.
-      expect(read.toString()).to.equal('ref:50-59');
-      expect(read.intersects(new ContigInterval('ref', 40, 49))).to.be.true;
-      expect(read.intersects(new ContigInterval('ref', 40, 48))).to.be.false;
+      expect(read.toString()).to.equal('insert:50-59');
+      expect(read.intersects(new ContigInterval('insert', 40, 49))).to.be.true;
+      expect(read.intersects(new ContigInterval('insert', 40, 48))).to.be.false;
       expect(read.intersects(new ContigInterval('0', 40, 55))).to.be.false;
-      expect(read.intersects(new ContigInterval('ref', 58, 60))).to.be.true;
-      expect(read.intersects(new ContigInterval('ref', 59, 60))).to.be.false;
+      expect(read.intersects(new ContigInterval('insert', 58, 60))).to.be.true;
+      expect(read.intersects(new ContigInterval('insert', 59, 60))).to.be.false;
     });
   });
 });

test/TwoBitDataSource-test.js

@@ -33,6 +33,7 @@ describe('TwoBitDataSource', function() {
       'chr22:3': null,
       'chr22:4': null
     });
+    expect(source.getRangeAsString(range)).to.equal('....');
 
     source.on('newdata', () => {
       expect(source.getRange(range)).to.deep.equal({
@@ -41,6 +42,7 @@ describe('TwoBitDataSource', function() {
         'chr22:3': 'C',
         'chr22:4': 'A'
       });
+      expect(source.getRangeAsString(range)).to.equal('NTCA');
       done();
     });
     source.rangeChanged(range);

test/pileuputils-test.js

@@ -5,8 +5,10 @@ var expect = require('chai').expect;
 
 var _ = require('underscore');
 
-var {pileup, addToPileup} = require('../src/pileuputils'),
-    Interval = require('../src/Interval');
+var {pileup, addToPileup, getDifferingBasePairs} = require('../src/pileuputils'),
+    Interval = require('../src/Interval'),
+    Bam = require('../src/bam'),
+    RemoteFile = require('../src/RemoteFile');
 
 describe('pileuputils', function() {
   // This checks that pileup's guarantee is met.
@@ -84,4 +86,29 @@ describe('pileuputils', function() {
     checkGuarantee(reads, rows);
     expect(rows).to.deep.equal([0,1,2,0,2]);
   });
+
+  function getSamArray(url) {
+    return new Bam(new RemoteFile(url)).readAll().then(d => d.alignments);
+  }
+
+  it('should find differences between ref and read', function() {
+    return getSamArray('/test/data/test_input_1_a.bam').then(reads => {
+      var read = reads[0];
+      expect(read.pos).to.equal(49);
+      expect(read.getCigarString()).to.equal('10M');
+      //                                   0123456789
+      expect(read.getSequence()).to.equal('ATTTAGCTAC');
+      var ref =                           'TTTTAGCGAC';
+
+      expect(getDifferingBasePairs(read, ref)).to.deep.equal([
+        {pos: 49+0, basePair: 'A'},
+        {pos: 49+7, basePair: 'T'}
+      ]);
+
+      // More complex CIGAR strings are not supported yet.
+      var read3 = reads[3];
+      expect(read3.getCigarString()).to.equal('1S2I6M1P1I1P1I4M2I');
+      expect(getDifferingBasePairs(read3, ref)).to.deep.equal([]);
+    });
+  });
 });