verkkofillet.tl.graphIdx

Contents

verkkofillet.tl.graphIdx#

verkkofillet.tl.graphIdx(obj, graph='assembly.homopolymer-compressed.gfa', threads=1, GraphAligner_path='GraphAligner', working_directory='graphAlignment', prefix=None, diploid_heuristic_cache=None, seeds_mxm_cache=None, showOnly=False)[source]#

Index the graph for graph alignment.

Parameters:

  • graph – The path to the graph file. Default is “assembly.homopolymer-compressed.gfa”.

  • threads – The number of threads to use. Default is 1.

  • GraphAligner_path – The path to the GraphAligner executable. Default is “GraphAligner”.

  • prefix – The prefix for the output files. Default is None. If None, the graph name is used as the prefix.

  • diploid_heuristic_cache – The path to the diploid heuristic cache file. Default is None. If None, the prefix is used.

  • seeds_mxm_cache – The path to the seeds mxm cache file. Default is None. If None, the prefix is used.

  • showOnly – If True, the command is printed but not executed. Default is False.

Returns:

index files.

Contents