Modify print_unique_MEs_by_type (which currently merges MEIs by location + insertion sequence) to pay attention to the --require_unique_sequence and --require_unique_calu_lineu options. If only the latter is specified then the merge should be done by cALU/LINEu signature for Alu and LINE elements and by insertion sequence for SVAs.
Modify
print_unique_MEs_by_type(which currently merges MEIs by location + insertion sequence) to pay attention to the--require_unique_sequenceand--require_unique_calu_lineuoptions. If only the latter is specified then the merge should be done by cALU/LINEu signature for Alu and LINE elements and by insertion sequence for SVAs.