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mavis/summary/summary

filter_by_call_method()

Filters a set of breakpoint pairs to returns the call with the most evidence. Prefers contig evidence over spanning over split over flanking, etc.

def filter_by_call_method(bpp_list):

Args

  • bpp_list

group_events()

group events together and join data attributes

def group_events(events):

Args

  • events

group_by_distance()

groups a set of calls based on their proximity. Returns a new list of calls where close calls have been merged

def group_by_distance(calls, distances):

Args

  • calls
  • distances

annotate_with_dgv_bpp()

Given a list of breakpoint pairs (bpps) and bpps from another reference set, annotate the events that are within the set distance of both breakpoints

def annotate_with_dgv_bpp(
    bpps: List[BreakpointPair],
    dgv_regions_list: List[BreakpointPair],
    input_cluster_radius: int,
):

Args

  • bpps (List[BreakpointPair]): the list of BreakpointPair objects
  • dgv_regions_list (List[BreakpointPair]): the dgv reference regions specified by the MAVIS input file represented as BreakpointPairs
  • input_cluster_radius (int): Distance used in matching input SVs to reference SVs through clusterind, defined by summary.cluster_radius in the configuration file

annotate_with_dgv_bed()

Given a list of breakpoint pairs (bpps) and bpps from another reference set, annotate the events that are within the set distance of both breakpoints

def annotate_with_dgv_bed(
    bpps: List[BreakpointPair],
    dgv_regions_by_reference_name: Dict[Tuple[str], List[BioInterval]],
    input_cluster_radius: int,
):

Args

  • bpps (List[BreakpointPair]): the list of BreakpointPair objects
  • dgv_regions_by_reference_name (Dict[Tuple[str], List[BioInterval]]): the dgv reference regions specified by the bed input file represented as BioIntervals
  • input_cluster_radius (int): Distance used in matching input SVs to reference SVs through clusterind, defined by summary.cluster_radius in the configuration file

annotate_dgv()

Given a list of breakpoint pairs (bpps) and bpps from another reference set, annotate the events that are within the set distance of both breakpoints

def annotate_dgv(
    bpps: List[BreakpointPair],
    dgv_regions_by_reference_name: Dict[Tuple[str], Union[List[BreakpointPair], List[BioInterval]]],
    input_cluster_radius: int,
):

Args

  • bpps (List[BreakpointPair]): the list of BreakpointPair objects
  • dgv_regions_by_reference_name (Dict[Tuple[str], Union[List[BreakpointPair], List[BioInterval]]]): tuple of strings of chr name and its associated list of BreakpointPair/BioInterval objects specified by the MAVIS input file
  • input_cluster_radius (int): Distance used in matching input SVs to reference SVs through clusterind, defined by summary.cluster_radius in the configuration file

get_pairing_state()

given two libraries, returns the appropriate descriptor for their matched state

def get_pairing_state(
    current_protocol,
    current_disease_state,
    other_protocol,
    other_disease_state,
    is_matched=False,
    inferred_is_matched=False,
):

Args

  • current_protocol (PROTOCOL): the protocol of the current library
  • current_disease_state (DISEASE_STATUS): the disease status of the current library
  • other_protocol (PROTOCOL): protocol of the library being comparing to
  • other_disease_state (DISEASE_STATUS): disease status of the library being compared to
  • is_matched (bool): True if the libraries are paired
  • inferred_is_matched

Returns

  • (PAIRING_STATE): descriptor of the pairing of the two libraries