tools module

mavis.tools.SUPPORTED_TOOL = MavisNamespace(CHIMERASCAN='chimerascan', DEFUSE='defuse', DELLY='delly', MANTA='manta', MAVIS='mavis', PINDEL='pindel', TA='transabyss', _defns={}, _types={'MANTA': <class 'str'>, 'DELLY': <class 'str'>, 'TA': <class 'str'>, 'PINDEL': <class 'str'>, 'CHIMERASCAN': <class 'str'>, 'MAVIS': <class 'str'>, 'DEFUSE': <class 'str'>})

Supported Tools used to call SVs and then used as input into MAVIS

mavis.tools.convert_tool_output(input_file, file_type='mavis', stranded=False, log=<function devnull>, collapse=True, assume_no_untemplated=True)[source]

Reads output from a given SV caller and converts to a set of MAVIS breakpoint pairs. Also collapses duplicates