handling of insertions and deletions

enclone can recognize and display a single insertion or deletion in a contig relative to the
reference, so long as its length is divisible by three, is relatively short, and occurs within the
V segment, not too close to its right end.

These indels could be germline, however most such events are already captured in a reference
sequence.  Currently the donor reference code in enclone does not recognize indels.

SHM deletions are rare, and SHM insertions are even more rare.

Deletions are displayed using hyphens (-).  If you use the var option for cvars, the hyphens will
be displayed in base space, where they are initially observed.  For the AMINO option, the deletion
is first shifted by up to two bases, so that the deletion starts at a base position that is
divisible by three.  Then the deleted amino acids are shown as hyphens.

Insertions are shown only in amino acid space, in a special per-chain column called notes that
appears if there is an insertion.  Colored amino acids are shown for the insertion, and the
position of the insertion is shown.  The notation e.g.
ins = TFT at 46
means that TFT is inserted after the first 46 amino acids.  Since the first amino acid (which is a
start codon) is numbered 0, the insertion actually occurs after the amino acid numbered 45.