gamgee/doxygen/reference__iterator_8h_source.html

 #ifndef gamgee__reference_iterator__guard

 #define gamgee__reference_iterator__guard


 #include "fastq_iterator.h"

 #include "fastq_reader.h"


 namespace gamgee {


 class ReferenceIterator {

  public:

   ReferenceIterator(const std::string& filename) :

     m_iterator {FastqReader{filename}.begin()},

     m_sequence {*m_iterator}

   {}


   const char ref_base(const std::string& chromosome, const int one_based_location);


  private:

   FastqIterator m_iterator;

   Fastq& m_sequence;

 };


 } // namespace gamgee


 #endif /* gamgee__reference_iterator__guard */

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::FastqReader::begin
FastqIterator begin()
creates a FastqIterator pointing at the start of the input stream (needed by for-each loop) ...
Definition: fastq_reader.cpp:39

gamgee::ReferenceIterator
Utility class to access reference bases in a FastA-formatted reference genome.
Definition: reference_iterator.h:14

gamgee
Definition: exceptions.h:9

fastq_iterator.h

gamgee::ReferenceIterator::ref_base
const char ref_base(const std::string &chromosome, const int one_based_location)
return the reference base character at the desired location
Definition: reference_iterator.cpp:8

gamgee::ReferenceIterator::ReferenceIterator
ReferenceIterator(const std::string &filename)
Definition: reference_iterator.h:16