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mavis.tools

mavis.tools.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,
    file_type=SUPPORTED_TOOL.MAVIS,
    stranded=False,
    log=DEVNULL,
    collapse=True,
    assume_no_untemplated=True,
):

Args

  • fnames
  • file_type
  • stranded
  • log
  • collapse
  • assume_no_untemplated