A string that is the canonical representation
of the given deletion type. Return NA
and raise a warning if
there is an un-normalized representation of
the deletion of a repeat unit.
See FindDelMH for details.
(This seems to be very rare.)
Arguments
context
The deleted sequence plus ample surrounding
sequence on each side (at least as long as del.seq).
del.seq
The deleted sequence in context.
pos
The position of del.sequence in context.
trace
If > 0, then generate messages tracing
how the computation is carried out.
This function first handles deletions in homopolymers, then
handles deletions in simple repeats with
longer repeat units, (e.g. CACACACA, see
FindMaxRepeatDel),
and if the deletion is not in a simple repeat,
looks for microhomology (see FindDelMH).
See the code for unexported function CanonicalizeID
and the functions it calls for handling of insertions.