/usr/include/blasr/datastructures/alignmentset/SAMSupplementalQVList.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
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 | #ifndef _BLASR_SAMSUPPLEMENTALQVLIST_HPP_
#define _BLASR_SAMSUPPLEMENTALQVLIST_HPP_
#include "SMRTSequence.hpp"
#include "SAMQVConversion.hpp"
class SupplementalQVList {
public:
//enum QVList {InsertionQV=0x1, DeletionQV=0x2, SubstitutionQV=0x4, MergeQV=0x8, SubstitutionTag=0x10, DeletionTag=0x20};
//enum QVIndex {I_InsertionQV=1,I_DeletionQV=2,I_SubstitutionQV=3,I_MergeQV=4,I_SubstitutionTag=5,I_DeletionTag=6};
//defined in FASTQSequence.
unsigned int useqv;
void SetDefaultQV() {
useqv = InsertionQV | DeletionQV | SubstitutionQV | MergeQV | DeletionTag;
}
static const char* qvTags[];
static const char* qvNames[];
static int nqvTags;
static int nTags;
int UseQV(std::vector<std::string> &qvList);
void FormatQVOptionalFields(SMRTSequence &alignedSubsequence);
void PrintQVOptionalFields(SMRTSequence &alignedSubsequence, std::ostream &out);
void clear();
};
#endif
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