/usr/include/pbseq/pbdata/sam/ReferenceSequence.hpp is in libpbdata-dev 0~20161219-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 | #ifndef _BLASR_SAM_REFERENCE_SEQUENCE_HPP_
#define _BLASR_SAM_REFERENCE_SEQUENCE_HPP_
#include <string>
#include "SAMKeywordValuePair.hpp"
class SAMReferenceSequence {
public:
std::string sequenceName;
uint64_t length;
std::string GetSequenceName() {
return sequenceName;
}
//
// By definining accessor functions here but no data, we can
// economize on the amount of space used for each element. This is
// no big deal for references, but for pairwise alignments, it is
// big.
//
std::string GetMD5() {
return "";
}
uint64_t GetLength() {
return length;
}
std::string GetGenomeAssembly() {
return "";
}
std::string GetSpecies() {
return "";
}
std::string GetURI() {
return "";
}
enum SAMReferenceSequenceRequiredFields { SQ_SN, SQ_LN };
static const char* SAMReferenceSequenceFieldNames[];
void StoreValues(std::vector<SAMKeywordValuePair> &kvPairs,
uint64_t lineNumber=0);
};
class SAMFullReferenceSequence : public SAMReferenceSequence {
public:
std::string md5;
std::string species;
std::string uri;
std::string genomeAssembly;
std::string GetMD5() {
return md5;
}
std::string GetSpecies() {
return species;
}
std::string GetURI() {
return uri;
}
std::string GetGenomeAssembly() {
return genomeAssembly;
}
enum FullReferenceSequenceRequiredFields { SQ_AS, SQ_M5, SQ_SP, SQ_UR };
static const char* SAMFullReferenceSequenceFieldNames[];
void StoreValues(std::vector<SAMKeywordValuePair> &kvPairs, uint64_t lineNumber=0);
};
#endif
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