Support for fasta input

[rsharris]

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I found that your code generates sequences conceptually; is there any way to obtain those sequences in a *.FASTA file?

[rsharris]

simulate_nucleotide_errors and simulate_nucleotide_errors_thm5 have --mutated= options, which will write the mutated sequences to a fasta file.

simulate_unit_errors and simulate_unit_errors_thm5 don't create nucleotide sequences. Instead, they work with a list of mutation positions. They don't have anything that could be reported as fasta. Looking at the code, I see that I included a debug option (--debug=mutated) that will write the list of error positions to stderr. So while that debug output isn't something we intend to document or support, you could potentially use that to create a fasta file.