René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Not a gzipped file","articleBody":"Hi,\n\nI received the following error when trying to read a standard bgzipped VCF file in kage:\n\n```\nFile \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/kage/command_line_interface.py\", line 52, in main\n    run_argument_parser(sys.argv[1:])\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/kage/command_line_interface.py\", line 559, in run_argument_parser\n    args.func(args)\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/kage/indexing/main.py\", line 305, in make_index_cli\n    r = make_index(args.reference, args.vcf, args.out_base_name,\n        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/kage/indexing/main.py\", line 74, in make_index\n    validate_input_vcf(vcf_file_name)\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/kage/indexing/main.py\", line 40, in validate_input_vcf\n    with bnp.open(vcf_file_name) as f:\n         ^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/bionumpy/io/files.py\", line 183, in bnp_open\n    return _get_buffered_file(filename, suffix, mode, is_gzip=is_gzip, buffer_type=buffer_type, lazy=lazy)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/bionumpy/io/files.py\", line 68, in _get_buffered_file\n    file_reader = NumpyFileReader(open_func(filename, \"rb\"), buffer_type) # , **kwargs2)\n                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/bionumpy/io/parser.py\", line 68, in __init__\n    self._header_data = self._buffer_type.read_header(self._file_obj)\n                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/site-packages/bionumpy/io/file_buffers.py\", line 163, in read_header\n    file_object.seek(-len(line), 1)\n  File \"/home/kevin/miniforge3/envs/kage/lib/python3.12/gzip.py\", line 421, in seek\n    return self._buffer.seek(offset, whence)\n           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^\ngzip.BadGzipFile: Not a gzipped file (b'\\x00\\x00')\n```\n\nIt took me a while to track the issue down, but it seems this was due to the use of the isal igzip module. As soon as I replaced the import with the standard gzip module everything worked fine. Let me know if there are any other details that might be helpful.","author":{"url":"https://github.com/lordkev","@type":"Person","name":"lordkev"},"datePublished":"2025-01-25T08:10:45.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":0},"url":"https://github.com/84/bionumpy/issues/84"}