1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/854e160efc7b/ changeset: 854e160efc7b user: jgoecks date: 2012-02-22 22:04:12 summary: Bug fixes for ac77414506d4 affected #: 2 files

diff -r ac77414506d4fb46197cb6db6f86707cfa78d21e -r 854e160efc7bd2b42eeb847057214bc92cec809f lib/galaxy/datatypes/converters/bgzip.py --- a/lib/galaxy/datatypes/converters/bgzip.py +++ b/lib/galaxy/datatypes/converters/bgzip.py @@ -26,8 +26,8 @@ if options.chrom_col and options.start_col and options.end_col: sort_params = ["sort", "-k%(i)s,%(i)s" % { 'i': options.chrom_col }, - "-k%(i)i,%(i)sn" % { 'i': options.start_col }, - "-k%(i)i,%(i)sn" % { 'i': options.end_col } + "-k%(i)i,%(i)in" % { 'i': options.start_col }, + "-k%(i)i,%(i)in" % { 'i': options.end_col } ] elif options.preset == "bed": sort_params = ["sort", "-k1,1", "-k2,2n", "-k3,3n"]

diff -r ac77414506d4fb46197cb6db6f86707cfa78d21e -r 854e160efc7bd2b42eeb847057214bc92cec809f lib/galaxy/datatypes/converters/interval_to_tabix_converter.py --- a/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py +++ b/lib/galaxy/datatypes/converters/interval_to_tabix_converter.py @@ -27,9 +27,9 @@ ctabix.tabix_index(filename=index_fname, preset=options.preset, keep_original=True, already_compressed=True, index_filename=out_fname) else: - # For interval files. - ctabix.tabix_index(filename=index_fname, seq_col=options.chrom_col, - start_col=options.start_col, end_col=options.end_col, + # For interval files; column indices are 0-based. + ctabix.tabix_index(filename=index_fname, seq_col=(options.chrom_col - 1), + start_col=(options.start_col - 1), end_col=(options.end_col - 1), keep_original=True, already_compressed=True, index_filename=out_fname) if os.path.getsize(index_fname) == 0: sys.stderr.write("The converted tabix index file is empty, meaning the input data is invalid.")

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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