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Initialization and Usage

Amplicons.__init__(reads, ...) Class to represent amplicon data.
Amplicons.__str__() Return the str representation of the Amplicons.
Amplicons.__len__() Return the number of amplicons in the amplicon-set.
Amplicons.__getitem__(index) Return the amplicon at the given index.
Amplicons.__iter__() Return an iterator for the amplicon-set. Returns the next amplicon in iteration.
Amplicons.span The fraction of the reference the amplicons span.
Amplicons.min_coverage The minimum coverage defined by amplicon-set.
Amplicons.score The score of the currently defined amplicon-set given the read-data.
Amplicons.calc_score(avg_cov, std_cov, ...) Calculates the score of the amplicons set.
Amplicons.is_valid(starts, ends) Determins whether the given configuration is valid.
Amplicons.get_reference_len() Get the length of the reference the reads are aligned to.
Amplicons.get_start_end_positions() Get the start and ending positions of the amplicons.
Amplicons.get_start_end_position(amplicon_index) Get the start and end position of the amplicon.
Amplicons.estimate_amplicons(reads, ...[, ...]) Estimate the amplicons given the read data via Monte-Carlo method.
Amplicons.amplicons_from_windows(reads, ...) Build candidate amplicons from the defined window sizes.
Amplicons.random_amplicons(reads, avg_len, ...) Generate amplicons from a random overlapping scheme for reads.
Amplicons.build_uniform_amplicons(reads, ...) Generate amplicons that have uniform length and overlap.