gsa-engineering/gamgee/variant__writer_8h_source.html

 #ifndef __gamgee_variant_writer__

 #define __gamgee_variant_writer__


 #include <string>


 #include "variant.h"

 #include "variant_header.h"

 #include "htslib/vcf.h"


 namespace gamgee {


 class VariantWriter {


  public:


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


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


   ~VariantWriter();


   void add_record(const Variant& body);


   void add_header(const VariantHeader& header);


  private:

   htsFile* m_out_file;

   VariantHeader m_header;


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

   void write_header() const;


 };


 }

 #endif

gamgee::VariantWriter::add_header
void add_header(const VariantHeader &header)
Adds a header to the file stream.
Definition: variant_writer.cpp:21

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

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

variant.h

gamgee::VariantWriter::add_record
void add_record(const Variant &body)
Adds a record to the file stream.
Definition: variant_writer.cpp:26

gamgee::Variant
Utility class to manipulate a Variant record.
Definition: variant.h:16

gamgee::VariantHeader
Utility class to hold a variant header.
Definition: variant_header.h:18

variant_header.h

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