Add missing bam provider

lib/galaxy/visualization/tracks/data/bam.py

@@ -0,0 +1,24 @@
+import pkg_resources; pkg_resources.require( "pysam" )
+from pysam import csamtools
+from math import floor, ceil, log
+import logging
+
+class BamDataProvider( object ):
+    def __init__( self, index, original_dataset ):
+        self.log = logging.getLogger(__name__)
+        self.index = index
+        self.original_dataset = original_dataset
+        
+    def get_data( self, chrom, start, end, **kwargs ):
+        start, end = int(start), int(end)
+        bamfile = csamtools.Samfile(filename=self.original_dataset.file_name, mode='rb', index_filename=self.index.file_name)
+        
+        data = bamfile.fetch(start=start, end=end, reference=chrom)
+        results = []
+        for read in data:
+            payload = { 'uid': str(read.pos) + str(read.seq), 'start': read.pos, 'end': read.pos + read.rlen, 'name': read.seq }
+            
+            results.append(payload)
+        bamfile.close()
+        return results
+