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mavis/convert/init

convert_tool_output()

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

def convert_tool_output(
    fnames: List[str],
    file_type: str = SUPPORTED_TOOL.MAVIS,
    stranded: bool = False,
    collapse: bool = True,
    assume_no_untemplated: bool = True,
) -> List[BreakpointPair]:

Args

  • fnames (List[str])
  • file_type (str)
  • stranded (bool)
  • collapse (bool)
  • assume_no_untemplated (bool)

Returns