cleanup

hammerlab · Apr 17, 2015 · 2037f41 · 2037f41
1 parent d0f4fd8
commit 2037f41
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Showing 2 changed files with 10 additions and 19 deletions.
diff --git a/src/SamRead.js b/src/SamRead.js
@@ -49,7 +49,7 @@ class SamRead {
 
   toString(): string {
     var stop = this.pos + this.l_seq;
-    return `${this.refID}:${this.pos}-${stop}`;
+    return `${this.refID}:${1+this.pos}-${stop}`;
   }
 
   _getJDataView(): jDataView {
@@ -70,10 +70,6 @@ class SamRead {
     var jb = new jBinary(this.buffer, bamTypes.TYPE_SET);
     return jb.read(bamTypes.ThickAlignment, 0);
   }
-
-  intersects(range: ContigInterval<string>): boolean {
-    return false;
-  }
 }
 
 module.exports = SamRead;
diff --git a/test/bam-test.js b/test/bam-test.js
@@ -62,11 +62,6 @@ describe('BAM', function() {
       done();
     }).done();
   });
-
-  function alignmentRange(alignment) {
-    var stop = alignment.pos + alignment.l_seq;
-    return `${alignment.refID}:${1+alignment.pos}-${stop}`;
-  }
 
   // This matches htsjdk's BamFileIndexTest.testSpecificQueries
   it('should find sequences using an index', function(done) {
@@ -77,11 +72,11 @@ describe('BAM', function() {
     var range = new ContigInterval('chrM', 10400, 10600);
     bam.getAlignmentsInRange(range, true).then(alignments => {
       expect(alignments).to.have.length(1);
-      expect(alignmentRange(alignments[0])).to.equal('0:10427-10477');
+      expect(alignments[0].toString()).to.equal('0:10427-10477');
       return bam.getAlignmentsInRange(range, false).then(alignments => {
         expect(alignments).to.have.length(2);
-        expect(alignmentRange(alignments[0])).to.equal('0:10388-10438');
-        expect(alignmentRange(alignments[1])).to.equal('0:10427-10477');
+        expect(alignments[0].toString()).to.equal('0:10388-10438');
+        expect(alignments[1].toString()).to.equal('0:10427-10477');
         done();
       });
     }).done();
@@ -104,7 +99,7 @@ describe('BAM', function() {
     bam.getAlignmentsInRange(range).then(reads => {
       // Note: htsjdk returns contig names like 'chr18', not 18.
       expect(reads).to.have.length(14);
-      expect(reads.map(alignmentRange)).to.deep.equal([
+      expect(reads.map(r => r.toString())).to.deep.equal([
           '18:3653516-3653566',
           '18:3653591-3653641',
           '18:4215486-4215536',
@@ -130,15 +125,15 @@ describe('BAM', function() {
     var range = new ContigInterval('chr1', 90002285, 116992285);
     bam.getAlignmentsInRange(range).then(reads => {
       expect(reads).to.have.length(92);
-      expect(reads.slice(0, 5).map(alignmentRange)).to.deep.equal([
+      expect(reads.slice(0, 5).map(r => r.toString())).to.deep.equal([
         '1:90071452-90071502',
         '1:90071609-90071659',
         '1:90622416-90622466',
         '1:90622572-90622622',
         '1:91182945-91182995'
       ]);
 
-      expect(reads.slice(-5).map(alignmentRange)).to.deep.equal([
+      expect(reads.slice(-5).map(r => r.toString())).to.deep.equal([
         '1:115379485-115379535',
         '1:116045704-116045754',
         '1:116045758-116045808',
@@ -158,7 +153,7 @@ describe('BAM', function() {
     // This verifies that alignments are tagged with the correct offset.
     var bam = new Bam(new RemoteFile('/test/data/index_test.bam'));
     bam.readAtOffset(new VirtualOffset(28269, 2247)).then(read => {
-      expect(alignmentRange(read)).to.equal('1:116563944-116563994');
+      expect(read.toString()).to.equal('1:116563944-116563994');
       done();
     }).done();
   });
@@ -195,8 +190,8 @@ describe('BAM', function() {
 
     bam.getAlignmentsInRange(range).then(reads => {
       expect(reads).to.have.length(1114);
-      expect(alignmentRange(reads[0])).to.equal('19:31511251-31511351');
-      expect(alignmentRange(reads[1113])).to.equal('19:31514171-31514271');
+      expect(reads[0].toString()).to.equal('19:31511251-31511351');
+      expect(reads[1113].toString()).to.equal('19:31514171-31514271');
       done();
     }).done();
   });