Character not occuring in the indexed text

[koeppl]

Let R be the reference string(s) we will index, and let S be the query string(s).
If S contains a character that does not occur in R, then when computing the matching statistics of S w.r.t. R, PHONI crashes.

To build the index on test_ref.fa:

python3 phoni build -r ../data/test_ref.fa -g shaped

and to compute the matching statistics of test_coll.fa w.r.t. test_ref.fa:

python3 phoni ms -i ../data/test_ref.fa -p ../data/test_coll.fa -g shaped

used files:

test_ref.fa:

>R
ABCDEF

test_coll.fa:

>1
EFGAAA

By changing G into A-F, the error vanishes.