Finds the amplicon starting and ending positions
in the reference given the primers used for the experiments.
Parameters :
reference : Bio.Seq
The reference sequence used to align reads with.
primers : list of Bio.SeqRecord
List containing starting and ending primers for all
experiments. Primers should be ordered by the amplicon order
along the reference. Additionally each pair should be ordered
by starting primer then ending primer.
Returns :
se_positions : list of (int, int)
List of integer pairs indicating the starting and ending positions
for each amplicon in the reference.