gamgee/doxygen/reference__map_8h_source.html

 #ifndef gamgee__reference_map__guard

 #define gamgee__reference_map__guard


 #include <unordered_map>

 #include <vector>

 #include <string>


 #include "fastq_reader.h"

 #include "interval.h"


 namespace gamgee {


 class ReferenceMap : public std::unordered_map<std::string, std::string> {

  public:


   ReferenceMap(const std::string& filename);


   std::string get_sequence(const Interval& interval,

                             const bool reverse_strand = false

       )const;


  private:

   void load_reference_from_fastq_reader(gamgee::FastqReader& reader);

   void read_fastq(gamgee::FastqReader& reader);

 };


 }  // namespace gamgee


 #endif /* gamgee__reference_map__guard */

gamgee::Interval
Utility class to store an genomic location (Interval).
Definition: interval.h:19

gamgee::FastqReader
Utility class to read many Fastq records from a stream (e.g. Fastq file, stdin, ...) in a for-each loop in a for-each loop.
Definition: fastq_reader.h:36

fastq_reader.h

gamgee::ReferenceMap::ReferenceMap
ReferenceMap(const std::string &filename)
opens a fasta/fastq reference file and creates a ReferenceMap from it
Definition: reference_map.cpp:15

gamgee
Definition: exceptions.h:9

gamgee::ReferenceMap::get_sequence
std::string get_sequence(const Interval &interval, const bool reverse_strand=false) const
locates the DNA sequence for a given Interval
Definition: reference_map.cpp:25

gamgee::ReferenceMap
Utility class to create a reference object for all reference operations in Foghorn.
Definition: reference_map.h:18

interval.h