GLnexus/service_8h_source.html

 #ifndef GLNEXUS_SERVICE_H

 #define GLNEXUS_SERVICE_H


 #include <string>

 #include <vector>

 #include <map>

 #include <set>

 #include <memory>

 #include "types.h"

 #include "data.h"

 #include "service_config.h"


 namespace GLnexus {


 class Service {

     // pImpl idiom

     struct body;

     std::unique_ptr<body> body_;


     Service(BCFData& data);

     Service(const Service&) = delete;


 public:

     static Status Start(Metadata& metadata, BCFData& data, std::unique_ptr<Service>& svc);

     ~Service();


     Status discover_alleles(const std::string& sampleset, const range& pos, discovered_alleles& ans);


     Status discover_alleles(const std::string& sampleset, const std::vector<range>& ranges,

                             std::vector<discovered_alleles>& ans);


     Status genotype_sites(const genotyper_config& cfg, const std::string& sampleset, const std::vector<unified_site>& sites, const std::string& filename, consolidated_loss& dlosses);

 };


 }


 #endif

GLnexus::range
Genomic range (chromosome id, begin coordinate, end coordinate)
Definition: types.h:99

GLnexus::Metadata
Definition: data.h:23

GLnexus::BCFData
Definition: data.h:98

GLnexus::Service::discover_alleles
Status discover_alleles(const std::string &sampleset, const range &pos, discovered_alleles &ans)

GLnexus::genotyper_config
Definition: service_config.h:15

GLnexus::Status
Function status (return) codes.
Definition: types.h:30

GLnexus::Service
Definition: service.h:15

GLnexus::Service::genotype_sites
Status genotype_sites(const genotyper_config &cfg, const std::string &sampleset, const std::vector< unified_site > &sites, const std::string &filename, consolidated_loss &dlosses)
Genotype a set of samples at the given sites, producing a BCF file.
Definition: service.cc:388

GLnexus::Service::body
Definition: service.cc:20