checkQC.handlers.undetermined_percentage_handler module

class checkQC.handlers.undetermined_percentage_handler.UndeterminedPercentageHandler(*args, **kwargs)

Bases: checkQC.handlers.qc_handler.QCHandler

This handler will check that the percentage of undetermined reads on a lane is below the specified threshold. If there are no indexes specified for the lane, this will be skipped.

check_qc()

The check_qc method provides the core behaviour of the QCHandler. It should check the values provided to it and yield instances of QCHandlerReport (or continue, if there was nothing to report)

Returns:An instance of QCHandlerReport

collect(signal)

The implementing subclass should provide this method. It is up to instance receiving the data to decide how to handle it. Below is an example of how to handle a tuple with a key-value pair.

class MySubscriber(Subscriber):

    def __init__(self):
        self.results = []

    def collect(self, signal):
        key, value = signal
        if key == "my_key":
            self.results.append(value)

Returns:None

parser()

The UndeterminedPercentageHandler fetches its data from the Stats.json file

Returns:A list of a StatsJsonParser callable and a InteropParser