| 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. |
| Amplicons.next() | 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. |