1 #ifndef theplu_yat_omic_bam_header 2 #define theplu_yat_omic_bam_header 25 #include "config_bam.h" 31 #include YAT_SAM_HEADER 33 #include <boost/iterator/transform_iterator.hpp> 42 #ifndef YAT_HAVE_HTSLIB 44 bam_header_t * bam_hdr_dup(
const bam_header_t* other);
62 typedef std::map<std::string, std::string> strMap;
63 typedef std::map<std::string, strMap> strMap2;
80 #ifdef YAT_HAVE_RVALUE 98 void parse_region(
const std::string& reg,
int& tid,
int& begin,
115 const std::string& program_group(
const std::string&
id,
116 const std::string& key)
const;
134 const std::string& read_group(
const std::string&
id,
135 const std::string& key)
const;
148 const std::map<std::string, std::string>&
149 read_group(
const std::string&
id)
const;
163 typedef boost::transform_iterator<
165 strMap2::const_iterator>
194 const char* target_name(
size_t tid)
const;
199 uint32_t target_length(
size_t tid)
const;
206 std::string text(
void)
const;
218 void text(
const std::string& txt);
229 int32_t tid(
const std::string& name)
const;
234 int32_t n_targets(
void)
const;
241 #ifdef YAT_HAVE_RVALUE 249 #ifndef YAT_HAVE_HTSLIB 250 typedef bam_header_t bam_hdr_t;
253 mutable strMap2 read_group_;
254 mutable strMap2 program_group_;
259 const std::string& group(strMap2& map,
const std::string& type,
260 const std::string&
id,
261 const std::string& key)
const;
263 void update_group(strMap2& map,
const std::string& type)
const;
The Department of Theoretical Physics namespace as we define it.
Functor that return std::pair.first.
Definition: stl_utility.h:762
Definition: BamFile.h:252
Definition: BamFile.h:132