gsa-engineering/gamgee/sam__writer_8h_source.html

 #ifndef __gamgee_sam_writer__

 #define __gamgee_sam_writer__


 #include <string>


 #include "sam.h"

 #include "sam_header.h"

 #include "htslib/sam.h"


 namespace gamgee {


 class SamWriter {


  public:


   explicit SamWriter(const std::string& output_fname = "-", const bool binary = true);


   explicit SamWriter(const SamHeader& header, const std::string& output_fname = "-", const bool binary = true);


   ~SamWriter();


   void add_record(const Sam& body);


   void add_header(const SamHeader& header);


  private:

   htsFile* m_out_file;

   SamHeader m_header;


   static htsFile* open_file(const std::string& output_fname, const std::string& binary);

   void write_header() const;


 };


 }

 #endif

sam.h

gamgee::SamWriter::SamWriter
SamWriter(const std::string &output_fname="-", const bool binary=true)
Creates a new SamWriter using the specified output file name.
Definition: sam_writer.cpp:5

gamgee::SamHeader
Utility class to hold the header of a sam file.
Definition: sam_header.h:13

gamgee::SamWriter::add_record
void add_record(const Sam &body)
Adds a record to the file stream.
Definition: sam_writer.cpp:26

gamgee::SamWriter::add_header
void add_header(const SamHeader &header)
Adds a header to the file stream.
Definition: sam_writer.cpp:21

sam_header.h

gamgee::SamWriter::~SamWriter
~SamWriter()
takes care of closing the file/stream
Definition: sam_writer.cpp:17

gamgee::SamWriter
utility class to write out a SAM/BAM/CRAM file to any stream
Definition: sam_writer.h:16

gamgee::Sam
Utility class to manipulate a Sam record.
Definition: sam.h:19