1 #ifndef _theplu_yat_omic_fasta 2 #define _theplu_yat_omic_fasta 21 #include <htslib/faidx.h> 53 Fasta(
const std::string& fn);
63 std::string
name(
size_t i)
const;
105 int size(
void)
const;
114 std::shared_ptr<char> seq_;
134 std::shared_ptr<faidx_t> faidx_;
138 void fetch(
Sequence& seq,
const std::string& chr,
int begin,
int end)
const;
140 void throw_unknown_chr(
const std::string&)
const;
Fasta(const std::string &fn)
The Department of Theoretical Physics namespace as we define it.
int sequence_length(const std::string &name) const
bool present(const std::string &name) const
const char * const_iterator
const iterator is a const char*
Definition: Fasta.h:90
const_iterator end(void) const
std::string name(size_t i) const
char operator[](size_t i) const
wrapper class around struct faidx_t in libhts
Definition: Fasta.h:41
Sequence sequence(const std::string &chr) const
const_iterator begin(void) const