1 #ifndef theplu_yat_omic_bam_header 2 #define theplu_yat_omic_bam_header 28 #include <htslib/sam.h> 30 #include <boost/iterator/transform_iterator.hpp> 53 typedef std::map<std::string, std::string> strMap;
54 typedef std::map<std::string, strMap> strMap2;
105 const std::string& key)
const;
123 const std::string&
read_group(
const std::string&
id,
124 const std::string& key)
const;
137 const std::map<std::string, std::string>&
152 typedef boost::transform_iterator<
154 strMap2::const_iterator>
195 std::string
text(
void)
const;
207 void text(
const std::string& txt);
216 int32_t
tid(
const std::string& name)
const;
235 mutable strMap2 read_group_;
236 mutable strMap2 program_group_;
242 const std::string& group(strMap2& map,
const std::string& type,
243 const std::string&
id,
244 const std::string& key)
const;
246 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:764
Definition: BamFile.h:245
Definition: BamFile.h:134
class to iterate through a InBamFile
Definition: BamReadIterator.h:61