1 #ifndef theplu_yat_omic_bam_header
2 #define theplu_yat_omic_bam_header
25 #include "config_bam.h"
29 #include YAT_SAM_HEADER
38 #ifndef YAT_HAVE_HTSLIB
40 bam_header_t * bam_hdr_dup(
const bam_header_t* other);
103 const std::string& key)
const;
119 const std::string&
read_group(
const std::string&
id,
120 const std::string& key)
const;
144 std::string
text(
void)
const;
153 void text(
const std::string& txt);
164 int32_t
tid(
const std::string& name)
const;
177 #ifndef YAT_HAVE_HTSLIB
178 typedef bam_header_t bam_hdr_t;
181 typedef std::map<std::string, std::string> strMap;
182 typedef std::map<std::string, strMap> strMap2;
183 mutable strMap2 read_group_;
184 mutable strMap2 program_group_;
189 const std::string& group(strMap2& map,
const std::string& type,
190 const std::string&
id,
191 const std::string& key)
const;
Definition: BamFile.h:213
Definition: BamFile.h:118