Solo BAC end alignments are not handled correctly in get_tpf_sp_tp_with_bacs_inserted_in_sequences_and_gaps

[suryasaha]

Not using the Contains or Partial keyword in align_BACends_group_coords.pl so we get warnings and critical messages from tpf_solo
Warning: Segment too short. AEKE02023641.1 length 1 : 0..0 is under 10

Where it is assigning just one base from a WGS contig to the AGP.
SL2.50SC05925 1631525 1677570 65 W AEKE02023641.1 16935 62980 -
SL2.50SC05925 1677571 1694497 66 F AC244568.2 1 16927 +
SL2.50SC05925 1694498 1694498 67 W AEKE02023641.1 1 1 -

Should not assign 'CONTAINED' for partial alignments. Manually removing for now. Adding a default TYPE-2 gap between the end-aligned solo BAC and the next sequence if there is no overlap.

TODO: Do this in get_tpf_sp_tp_with_bacs_inserted_in_sequences_and_gaps

[suryasaha]

Also add message in STDERR about possible superfluous gap TPF line after BAC. User should try to remove it to see if the solo BAC end aligned BAC aligns to the next sequence in the TPF. Maybe use WARNING keyword in STDERR for manual post-processing.