dict.hpp File Reference

#include "genesis/sequence/reference_genome.hpp"
#include "genesis/sequence/sequence_dict.hpp"
#include "genesis/sequence/sequence_set.hpp"
#include "genesis/utils/io/input_source.hpp"
#include <string>
#include <vector>

Go to the source code of this file.

Namespaces
	genesis
	Container namespace for all symbols of genesis in order to keep them separate when used as a library.
	genesis::sequence

Enumerations
enum	ReferenceComparisonMode { kStrict, kLeftSuperset, kRightSuperset, kSharedOnly }
	Chose how to deal with sub-/super-sets when comparing references. More...

Functions
bool	compatible_references (SequenceDict const &lhs, SequenceDict const &rhs, ReferenceComparisonMode mode=ReferenceComparisonMode::kStrict)
	Verify that a SequenceDict fits a SequenceSet. More...
SequenceDict	read_sequence_dict (std::shared_ptr< utils::BaseInputSource > source)
	Read a .dict sequence dictionary file, describing, e.g., reference genome sequence properties. More...
SequenceDict	read_sequence_fai (std::shared_ptr< utils::BaseInputSource > source)
	Read a .fai sequence index file, describing, e.g., reference genome sequence properties. More...
SequenceDict	reference_genome_to_dict (ReferenceGenome const &rg)
	Get the sequence dict/index information of a given set of Sequences that are stored in a ReferenceGenome. More...
SequenceDict	sequence_set_to_dict (SequenceSet const &set)
	Get the sequence dict/index information of a given set of Sequences. More...
bool	verify (SequenceDict const &dict, SequenceSet const &set, bool match_first_word=false)
	Verify that a SequenceDict fits a SequenceSet. More...