bioa.io.amplicon.build_uniform_amplicons_from_file

build_uniform_amplicons_from_file(filename, amp_len, overlap, ref_len)

Creates the Amplicons data structure from a file of reads. The file structure must follow:

read, position

for this to operate correctly. This assumes that all neigboring amplicons have the same overlap.

Parameters :

filename : str

Path to the read-data file.

amp_len : int

Number of bases covered by a single amplicon.

overlap : int

The number of bases that neighboring amplicons overlap.

ref_len : int

Length of the entire reference genome.

Returns :

amplicons : bioa.Amplicons

Amplicon data structure containing all distinct reads and meta-data.