Merge pull request #470 from akmorrow13/fix-ga4gh-alignments

Updated GA4GHAlignment from v0.5.1 to v0.6.0a10

src/main/GA4GHAlignment.js

@@ -10,7 +10,8 @@ import type {CigarOp, MateProperties, Strand} from './Alignment';
 import ContigInterval from './ContigInterval';
 import SamRead from './data/SamRead';
 
-// See https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/common.avdl
+// See https://github.com/ga4gh/ga4gh-schemas/blob/master/src/main/proto/ga4gh/reads.proto
+// Data can be queried at http://1kg.ga4gh.org/reads/search
 var OP_MAP = {
   ALIGNMENT_MATCH: 'M',
   INSERT: 'I',
@@ -36,7 +37,7 @@ class GA4GHAlignment /* implements Alignment */ {
   _interval: ContigInterval<string>;
 
   // alignment follows org.ga4gh.GAReadAlignment
-  // https://github.com/ga4gh/schemas/blob/v0.5.1/src/main/resources/avro/reads.avdl
+  // https://github.com/ga4gh/ga4gh-schemas/blob/master/src/main/proto/ga4gh/reads.proto
   constructor(alignment: Object) {
     this.alignment = alignment;
     this.pos = parseInt(alignment.alignment.position.position);
@@ -56,7 +57,7 @@ class GA4GHAlignment /* implements Alignment */ {
   }
 
   getStrand(): Strand {
-    return this.alignment.alignment.position.reverseStrand ? '-' : '+';
+    return this.alignment.alignment.position.strand == 'NEG_STRAND' ? '-' : '+';
   }
 
   getQualityScores(): number[] {
@@ -83,8 +84,8 @@ class GA4GHAlignment /* implements Alignment */ {
     var next = this.alignment.nextMatePosition;
     return next && {
       ref: next.referenceName,
-      pos: next.position,
-      strand: next.reverseStrand ? '-' : '+'
+      pos: parseInt(next.position),
+      strand: next.strand == 'NEG_STRAND' ? '-' : '+'
     };
   }
 

src/test/GA4GHAlignment-test.js

@@ -11,63 +11,69 @@ describe('GA4GHAlignment', function() {
   var sampleAlignments = [];
 
   before(function() {
-    return new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json').getAllString().then(data => {
+    return new RemoteFile('/test-data/alignments.ga4gh.1.10000-11000.json').getAllString().then(data => {
       sampleAlignments = JSON.parse(data).alignments;
     });
   });
 
   it('should read the sample alignments', function() {
-    expect(sampleAlignments).to.have.length(14);
+    expect(sampleAlignments).to.have.length(100);
   });
 
   it('should provide basic accessors', function() {
     var a = new GA4GHAlignment(sampleAlignments[0]);
-    expect(a.name).to.equal('r000');
-    expect(a.getSequence()).to.equal('ATTTAGCTAC');
-    expect(a.getQualityScores()).to.deep.equal([32,32,32,32,32,32,32,32,32,32]);
+    expect(a.name).to.equal('ERR181329.21587964');
+    expect(a.getSequence()).to.equal('ATAACCCTAACCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA');
+    expect(a.getQualityScores()).to.deep.equal([2, 36, 36, 37, 37, 38, 37, 39, 37, 38, 38, 38, 3, 38, 38, 39, 38, 39, 39, 39, 38, 39, 39, 38, 40, 40, 38, 39, 39, 39, 39, 40, 38, 40, 39, 40, 38, 38, 38, 39, 38, 40, 37, 40, 38, 39, 39, 40, 40, 40, 39, 32, 39, 35, 39, 36, 38, 40, 39, 39, 39, 36, 39, 37, 39, 40, 39, 31, 39, 35, 36, 39, 37, 32, 40, 41, 38, 38, 37, 32, 39, 38, 38, 39, 33, 36, 25, 37, 38, 19, 35, 13, 37, 31, 35, 33, 34, 8, 33, 18]);
     expect(a.getStrand()).to.equal('+');
-    expect(a.getInterval().toString()).to.equal('chr17:4-13');  // 0-based
+    expect(a.getInterval().toString()).to.equal('1:9999-10098');  // 0-based
     expect(a.cigarOps).to.deep.equal([
-      {op: 'M', length: 10}
+      {op: 'M', length: 100}
     ]);
     expect(a.getMateProperties()).to.deep.equal({
-      ref: 'chr17',
-      pos: 79,
-      strand: '+'
+      ref: '1',
+      pos: 10007,
+      strand: '-'
     });
   });
 
   it('should match SamRead', function() {
     var bam = new Bam(new RemoteFile('/test-data/chr17.1-250.bam'));
-    return bam.readAll().then(({alignments: samReads}) => {
-      // This is a workaround. See https://github.com/ga4gh/server/issues/488
-      samReads.splice(-1, 1);
+    var json = new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json');
 
-      expect(sampleAlignments.length).to.equal(samReads.length);
-      for (var i = 0; i < sampleAlignments.length; i++) {
-        var ga4gh = new GA4GHAlignment(sampleAlignments[i]),
-            bam = samReads[i];
-        expect(ga4gh.getSequence()).to.equal(bam.getSequence());
-        var interval = ga4gh.getInterval();
-        expect(interval.start()).to.equal(bam.pos);
+    json.getAllString().then(data => {
+      var matchingBamAlignments = JSON.parse(data).alignments;
 
-        // See https://github.com/ga4gh/server/issues/491
-        // expect(ga4gh.getStrand()).to.equal(bam.getStrand());
-        // For the if statement, see https://github.com/ga4gh/server/issues/492
-        var quality = ga4gh.getQualityScores();
-        if (quality.length) {
-          expect(quality).to.deep.equal(bam.getQualityScores());
-        }
-        expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps);
-        // After ga4gh#491, change this to a .deep.equal on getMateProperties()
-        var ga4ghMate = ga4gh.getMateProperties(),
-            bamMate = bam.getMateProperties();
-        expect(!!ga4ghMate).to.equal(!!bamMate);
-        if (ga4ghMate && bamMate) {
-          expect(ga4ghMate.ref).to.equal(bamMate.ref);
-          expect(ga4ghMate.pos).to.equal(bamMate.pos);
+      return bam.readAll().then(({alignments: samReads}) => {
+        // This is a workaround. See https://github.com/ga4gh/server/issues/488
+        samReads.splice(-1, 1);
+
+        expect(matchingBamAlignments.length).to.equal(samReads.length);
+        for (var i = 0; i < matchingBamAlignments.length; i++) {
+          var ga4gh = new GA4GHAlignment(matchingBamAlignments[i]),
+              bam = samReads[i];
+          expect(ga4gh.getSequence()).to.equal(bam.getSequence());
+          var interval = ga4gh.getInterval();
+          expect(interval.start()).to.equal(bam.pos);
+
+          // See https://github.com/ga4gh/server/issues/491
+          // expect(ga4gh.getStrand()).to.equal(bam.getStrand());
+          // For the if statement, see https://github.com/ga4gh/server/issues/492
+          var quality = ga4gh.getQualityScores();
+          if (quality.length) {
+            expect(quality).to.deep.equal(bam.getQualityScores());
+          }
+          expect(ga4gh.cigarOps).to.deep.equal(bam.cigarOps);
+          // After ga4gh#491, change this to a .deep.equal on getMateProperties()
+          var ga4ghMate = ga4gh.getMateProperties(),
+              bamMate = bam.getMateProperties();
+          expect(!!ga4ghMate).to.equal(!!bamMate);
+          if (ga4ghMate && bamMate) {
+            expect(ga4ghMate.ref).to.equal(bamMate.ref);
+            expect(ga4ghMate.pos).to.equal(bamMate.pos);
+          }
         }
-      }
+      });
     });
   });
 });

src/test/sources/GA4GHAlignmentSource-test.js

@@ -13,7 +13,7 @@ describe('GA4GHAlignmentSource', function() {
   var server: any = null, response;
 
   before(function () {
-    return new RemoteFile('/test-data/alignments.ga4gh.chr17.1-250.json').getAllString().then(data => {
+    return new RemoteFile('/test-data/alignments.ga4gh.1.10000-11000.json').getAllString().then(data => {
       response = data;
       server = sinon.fakeServer.create();  // _after_ we do a real XHR!
     });
@@ -24,16 +24,16 @@ describe('GA4GHAlignmentSource', function() {
   });
 
   it('should fetch alignments from a server', function(done) {
-    server.respondWith('POST', '/v0.5.1/reads/search',
+    server.respondWith('POST', '/v0.6.0a10/reads/search',
                        [200, { "Content-Type": "application/json" }, response]);
 
     var source = GA4GHAlignmentSource.create({
-      endpoint: '/v0.5.1',
+      endpoint: '/v0.6.0a10',
       readGroupId: 'some-group-set:some-read-group',
       forcedReferenceId: null
     });
 
-    var requestInterval = new ContigInterval('chr17', 10, 20);
+    var requestInterval = new ContigInterval('1', 10000, 10007);
     expect(source.getAlignmentsInRange(requestInterval))
         .to.deep.equal([]);
 
@@ -42,11 +42,11 @@ describe('GA4GHAlignmentSource', function() {
     source.on('networkdone', e => { progress.push('done'); });
     source.on('newdata', () => {
       var reads = source.getAlignmentsInRange(requestInterval);
-      expect(reads).to.have.length(1);
+      expect(reads).to.have.length(16);
       done();
     });
 
-    source.rangeChanged({contig: 'chr17', start: 1, stop: 30});
+    source.rangeChanged({contig: '1', start: 10000, stop: 10007});
     server.respond();
   });
 

test-data/README.md

@@ -62,9 +62,16 @@ corresponding SAM files for them in the same repo.
 This was hand-edited from the SAM equivalent of `test_input_1_a.bam` to have
 reads in chr17:1-250. It was then converted back to BAM/BAI using `samtools view`.
 
-The JSON variant was formed by loading `chr17.1-250.bam` into v0.5.1 of the [GA4GH demo server][ga4gh] and querying for all the reads via:
+The JSON variant was formed by loading `chr17.1-250.bam` into 0.6.0a10 of the [GA4GH demo server][ga4gh] and querying for all the reads via:
 
-    curl --data '{"readGroupIds":["pileup.js:chr17.1-250"]}' --header 'Content-Type: application/json' http://localhost:8000/v0.5.1/reads/search > alginments.ga4gh.chr17.1-250.json
+    curl --data '{"readGroupIds":["pileup.js:chr17.1-250"]}' --header 'Content-Type: application/json' http://localhost:8000/0.6.0a10/reads/search > alignments.ga4gh.chr17.1-250.json
+
+
+#### alignments.ga4gh.1.10000-11000.json
+
+alignments.ga4gh.1.10000-11000.json was generated from the 0.6.0a10 GA4GH server http://1kgenomes.ga4gh.org/reads/search with the following
+parameters:
+{"readGroupIds": ["WyIxa2dlbm9tZXMiLCJyZ3MiLCJIRzAzMjcwIiwiRVJSMTgxMzI5Il0"], "referenceId": "WyJOQ0JJMzciLCIxIl0"}
 
 #### index_test.bam