Comments to describe .coords file format
Support for custom symbols for non-SNP columns
Add --outfile support + fix --symbol check bug
Support for .gz compressed reference (1st FASTA) but not others yet
Full support for compressed .gz FASTA files
Change default output format to (aligned) FASTA
Disable --distant option as promer doesn't give nucleotide coordinates!
MAJOR FIX: wasn't masking off unaligned regions