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Hi Ryan
As we discussed I have implemented hairpin read-through for linear contigs with a
hairpin_left=trueorhairpin_right=truein the FASTA header. I decided to only allow a single read-through, so currently multi-passes for a contig with two hairpins is not implemented.I have added relevant unit tests to the testfragments.py. Additionally, I have updated several tests/modules to use the updated functions for load_fasta and load_reference since they now also return information on hairpins.