When running gramtools build with --ref <ref.fa> and <ref.fa> contains 'N' bases (or indeed anything else than A/C/G/T) we get:
2021-03-01 17:27:35,872 gramtools ERROR Did not receive a nucleotide: N not in {A,C,G,T}
2021-03-01 17:27:35,872 gramtools ERROR Unsuccessful vcf_to_PRG_string_conversion.
The current recommended workaround is to replace these with a given base, eg replace all 'N's with 'C's.
A possible fix is to use a dedicated integer for non-A/C/G/T bases in the binary prg string, which should trigger read mapping to fail when reached.
When running
gramtools buildwith--ref <ref.fa>and<ref.fa>contains 'N' bases (or indeed anything else than A/C/G/T) we get:The current recommended workaround is to replace these with a given base, eg replace all 'N's with 'C's.
A possible fix is to use a dedicated integer for non-A/C/G/T bases in the binary prg string, which should trigger read mapping to fail when reached.