Commit 08bb9722 authored by Lucille Delisle's avatar Lucille Delisle
Browse files

fix column indices

parent 271179b3

lib/galaxy/datatypes/tabular.py

+5 −4
Original line number Diff line number Diff line
@@ -1829,17 +1829,18 @@ class Tabix(Tabular): 
                )



            try:

                # tabix_index columns are 0-based while in the command line it is 1-based

                pysam.tabix_index(

                    dataset.file_name,

                    index=index_file.file_name,

                    seq_col=dataset.metadata.chromCol,

                    start_col=dataset.metadata.startCol,

                    end_col=dataset.metadata.endCol,

                    seq_col=dataset.metadata.chromCol - 1,

                    start_col=dataset.metadata.startCol - 1,

                    end_col=dataset.metadata.endCol - 1,

                    keep_original=True,

                    force=True,

                )

            except Exception as e:

                raise Exception(f"Error setting VCF.gz metadata: {util.unicodify(e)}")

                raise Exception(f"Error setting tabix metadata: {util.unicodify(e)}")

            else:

                dataset.metadata.tabix_index = index_file