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mavis/config

class CustomHelpFormatter

inherits argparse.ArgumentDefaultsHelpFormatter

subclass the default help formatter to stop default printing for required arguments

class RangeAppendAction

inherits argparse.Action

allows an argument to accept a range of arguments

RangeAppendAction.__init__()

def __init__(self, nmin=1, nmax=None, **kwargs):

Args

  • nmin
  • nmax

calculate_bam_stats()

Calculate the read stats for a library from a given bam file

def calculate_bam_stats(config: Dict, library_name: str) -> Dict:

Args

  • config (Dict)
  • library_name (str)

Returns

  • Dict

add_bamstats_to_config()

Check that the input JSON config conforms to the expected schema as well as the other relevant checks such as file exsts

def add_bamstats_to_config(config: Dict):

Args

  • config (Dict)

get_metavar()

For a given argument type, returns the string to be used for the metavar argument in add_argument

def get_metavar(arg_type):

Args

  • arg_type

Examples

>>> get_metavar(bool)
'{True,False}'