1 #ifndef GENESIS_SEQUENCE_FORMATS_FASTA_READER_H_ 2 #define GENESIS_SEQUENCE_FORMATS_FASTA_READER_H_ 186 SequenceSet read( std::shared_ptr< utils::BaseInputSource > source )
const;
198 void read( std::shared_ptr< utils::BaseInputSource > source,
SequenceSet& sequence_set )
const;
246 bool parse_sequence_pedantic(
296 bool guess_abundances()
const;
315 FastaReader& valid_chars( std::string
const& chars );
322 std::string valid_chars()
const;
340 SiteCasing site_casing_ = SiteCasing::kToUpper;
341 bool guess_abundances_ =
false;
342 bool use_validation_ =
false;
350 #endif // include guard Read Fasta sequence data.
ParsingMethod
Enumeration of the available methods for parsing Fasta sequences.
Container namespace for all symbols of genesis in order to keep them separate when used as a library...
Store a set of Sequences.
SiteCasing
Enumeration of casing methods to apply to each site of a Sequence.
Default option, simply calculate the site entropy using the characters used in the SiteCounts object...