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Anonymous committed 8aa0ac9

Do not use tabix for GFF/GTF because tabix is woefully naive about these data formats.

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  • Parent commits 60d7ff7

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datatypes_conf.xml.sample

     <datatype extension="gif" type="galaxy.datatypes.images:Gif" mimetype="image/gif"/>
     <datatype extension="gmaj.zip" type="galaxy.datatypes.images:Gmaj" mimetype="application/zip"/>
     <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true">
-        <converter file="gff_to_bgzip_converter.xml" target_datatype="bgzip"/>
-        <converter file="gff_to_tabix_converter.xml" target_datatype="tabix" depends_on="bgzip"/>
+        <converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/>
         <converter file="gff_to_summary_tree_converter.xml" target_datatype="summary_tree"/>
     </datatype>
     <datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" />

lib/galaxy/datatypes/interval.py

         Gff.set_meta( self, dataset, overwrite = overwrite, skip = i )
         
     def get_track_type( self ):
-        return "FeatureTrack", {"data": "tabix", "index": "summary_tree"}
+        return "FeatureTrack", {"data": "interval_index", "index": "summary_tree"}
 
 
 class Wiggle( Tabular, _RemoteCallMixin ):