Hash bam features

src/JBrowse/Digest/Crc32.js

@@ -22,9 +22,27 @@ var Crc32 = {
         return re;
     },
 
-    crc32: function( str, crc ) {
+    crc32_raw: function( bytes, start, end, crc = 0 ) {
+        var n = 0; //a number between 0 and 255
+        var x = 0; //a hex number
+        var table = Crc32.crc32Table;
+
+        crc = crc ^ (-1);
+        for( var i = start, iTop = end; i < iTop; i++ ) {
+            n = ( crc ^ bytes[i] ) & 0xFF;
+            x = "0x" + table.substr( n * 9, 8 );
+            crc = ( crc >>> 8 ) ^ x;
+        }
+        crc = crc ^ (-1);
+        //convert to unsigned 32-bit int if needed
+        if (crc < 0) {
+            crc += 4294967296;
+        }
+        return crc;
+    },
+
+    crc32: function( str, crc = 0 ) {
         var bytes = Crc32.stringToBytes(str);
-        if( crc == window.undefined ) crc = 0;
         var n = 0; //a number between 0 and 255
         var x = 0; //a hex number
         var table = Crc32.crc32Table;
@@ -62,4 +80,4 @@ var Crc32 = {
 };
 
 return Crc32;
-});
+});

src/JBrowse/Store/SeqFeature/BAM/LazyFeature.js

@@ -1,9 +1,10 @@
 define( ['dojo/_base/array',
          'JBrowse/Util',
+         'JBrowse/Digest/Crc32',
          './Util',
          'JBrowse/Model/SimpleFeature'
         ],
-        function( array, Util, BAMUtil, SimpleFeature ) {
+        function( array, Util, Crc32, BAMUtil, SimpleFeature ) {
 
 var SEQRET_DECODER = ['=', 'A', 'C', 'x', 'G', 'x', 'x', 'x', 'T', 'x', 'x', 'x', 'x', 'x', 'x', 'N'];
 var CIGAR_DECODER  = ['M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X', '?', '?', '?', '?', '?', '?', '?'];
@@ -100,7 +101,7 @@ 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');
+        return Crc32.crc32_raw(this.bytes.byteArray, this.bytes.start, this.bytes.end);
     },
 
     multi_segment_all_aligned: function() {

tests/data/duplicate_bam_features_tomato/seq/refSeqs.json

@@ -0,0 +1 @@
+[{"end":13350063,"length":13350063,"name":"SL2.50ch03","start":0}]

tests/data/duplicate_bam_features_tomato/tracks.conf

@@ -0,0 +1,4 @@
+[tracks.tomato_bam]
+urlTemplate=six_tomato_reads.bam
+type=Alignments2
+hideSecondary=false