make BAM feature IDs truly unique. should have thought of this 6 year…

…s ago. (cc @cmdcolin)
GMOD · Jul 3, 2018 · 0b148fd · 0b148fd
1 parent fd86983
commit 0b148fd
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diff --git a/release-notes.md b/release-notes.md
@@ -5,6 +5,9 @@
  * Fixed a memory leak that was introduced in JBrowse 1.13.1 in generate-names.pl. Thanks to
    @scottcain for reporting (issue #1058, @cmdcolin).
 
+ * Fixed a bug in which duplicate BAM features would sometimes not be shown separately in the
+   view if they contain the same data. (@rbuels)
+
 # Release 1.14.2     2018-06-04 23:41:52 UTC
 
 ## Minor improvements

diff --git a/src/JBrowse/Store/SeqFeature/BAM/File.js b/src/JBrowse/Store/SeqFeature/BAM/File.js
@@ -449,7 +449,8 @@ var BamFile = declare( null,
                     var feature = new BAMFeature({
                         store: this.store,
                         file: this,
-                        bytes: { byteArray: ba, start: blockStart, end: blockEnd }
+                        bytes: { byteArray: ba, start: blockStart, end: blockEnd },
+                        featureNumber: featureCount,
                      });
                     sink.push(feature);
                     featureCount++;

diff --git a/src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js b/src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js
@@ -27,6 +27,8 @@ var Feature = Util.fastDeclare(
             byteArray: args.bytes.byteArray
         };
 
+        this.featureNumber = args.featureNumber // feature number within the block
+
         this._coreParse();
     },
 
@@ -100,7 +102,10 @@ var Feature = Util.fastDeclare(
     },
 
     id: function() {
-        return this._get('name')+'/'+this._get('md')+'/'+this._get('cigar')+'/'+this._get('start')+'/'+this._get('multi_segment_next_segment_reversed');
+        // the guaranteed unique ID of the feature is the byte
+        // offset in the file of the block that it is in,
+        // plus the sequential number of this feature's place in the block.
+        return `${this.bytes.start}-${this.featureNumber}`
     },
 
     multi_segment_all_aligned: function() {