FaiToReferenceLengths reads in a fasta fai file and returns a map of reference name to reference length.

GenerateIndex generates an index (*.fai) from FASTA.

New creates a new Fasta that holds all the FASTA data from the given reader in memory.

NewIndexed creates a new Fasta that can perform efficient random lookups using the provided index, without reading the data into memory.

OptClean specifies returned FASTA sequences should be cleaned as described in biosimd.CleanASCIISeq*.

OptEncoding specifies the encoding of the in-memory FASTA sequences.

OptIndex makes New read FASTA file with a provided index, like NewIndexed.

CleanASCII encoding capitalizes all lowercase 'a'/'c'/'g'/'t', and converts all non-ACGT characters to 'N'.

TODO(cchang): Add 'Base5' encoding, where 'A'/'a' = 0, 'C'/'c' = 1, 'G'/'g' = 2, 'T'/'t' = 3, anything else = 4.

RawASCII encoding preserves the original bytes, including case.

Seq8 encoding is 'A'/'a' = 1, 'C'/'c' = 2, 'G'/'g' = 4, 'T'/'t' = 8, anything else = 15.

Fasta represents FASTA-formatted data, consisting of a set of named sequences.

Opt is an optional argument to New, NewIndexed.