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
- List[BreakpointPair]