multi-seqs spit out from partis partition are now accounted for (again) in flexbounds/relpos
in the case of single sequence, we still want padded sequences (for consistency across all CF sizes)
in the case of V/J FWK insertions and padding and its effect on flexbounds/relpos, that is manually accounted for in the code as S-W operates on the input sequences before removal of FWK insertions and addition of N-padding, but we would like to use indel-reversed-seqs (i.e. sequences with FWK insertions removed, indels reversed, and N-padding so they are all of equal length) for linearham.
partis partitionare now accounted for (again) in flexbounds/relposindel-reversed-seqs(i.e. sequences with FWK insertions removed, indels reversed, and N-padding so they are all of equal length) for linearham.Command:
bin/partis partition --infname testing_amrit/partis_input_seqs.fa --outfname testing_amrit/partis_output.yaml --parameter-dir _output --linearham