Handle Ns in sequence alignments

[ijhoskins]

I aligned my reads with the following parameters (based on 04/19/21 communication with Roujia Li):
bowtie2 --no-head --norc --no-sq --rdg 12,1 --rfg 12,1 --local

When running tileseq_sam2mut.pl on the resulting SAM files I get the following error:
Bad codon "TAN"!!

Thus it seems the variant calling script is calling mutations with N.