Merge pull request #1897 from dannon/pysam_compat

[16.01] Slight tweaks to our tabix usage.

lib/galaxy/visualization/data_providers/genome.py

@@ -196,7 +196,6 @@ class GenomeDataProvider( BaseDataProvider ):
         except AttributeError:
             # FIXME: some data providers do not have a close function implemented.
             # Providers without a close function include:
-            #  pysam Tabixfile
             #  bx IntervalIndex
             pass
 
@@ -347,13 +346,16 @@ class TabixDataProvider( FilterableMixin, GenomeDataProvider ):
 
     def open_data_file( self ):
         return ctabix.Tabixfile(self.dependencies['bgzip'].file_name,
-                                index_filename=self.converted_dataset.file_name)
+                                index=self.converted_dataset.file_name)
 
     def get_iterator( self, data_file, chrom, start, end, **kwargs ):
-        start, end = int(start), int(end)
+        # chrom must be a string, start/end integers.
+        # in previous versions of pysam, unicode was accepted for chrom, but not in 8.4
+        chrom = str(chrom)
+        start = int(start)
+        end = int(end)
         if end >= (2 << 29):
             end = (2 << 29 - 1)  # Tabix-enforced maximum
-
         # Get iterator using either naming scheme.
         iterator = iter( [] )
         if chrom in data_file.contigs: