/usr/include/pbseq/alignment/algorithms/anchoring/GlobalChain.hpp is in libblasr-dev 0~20161219-2.
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 28 29 30 31 32 33 34 35 36 37 38 39 | #ifndef _BLASR_GLOBAL_CHAIN_HPP_
#define _BLASR_GLOBAL_CHAIN_HPP_
#include <vector>
// pbdata
#include "../../../pbdata/Types.h"
#include "../../../pbdata/DNASequence.hpp"
#include "PrioritySearchTree.hpp"
template<typename T_Fragment, typename T_Endpoint>
void FragmentSetToEndpoints(T_Fragment* fragments, int nFragments,
std::vector<T_Endpoint> &endpoints);
template<typename T_Fragment>
UInt RestrictedGlobalChain(T_Fragment *fragments,
DNALength nFragments, float maxIndelRate,
std::vector<VectorIndex>& optFragmentChainIndices,
std::vector<UInt>& scores, std::vector<UInt>& prevOpt);
template<typename T_Fragment, typename T_Endpoint>
int GlobalChain( T_Fragment *fragments,
DNALength nFragments,
std::vector<VectorIndex> &optFragmentChainIndices,
std::vector<T_Endpoint> *bufEndpointsPtr = NULL);
template<typename T_Fragment, typename T_Endpoint>
int GlobalChain(std::vector<T_Fragment> &fragments,
std::vector<VectorIndex> &optFragmentChainIndices);
template<typename T_Fragment, typename T_Endpoint>
int GlobalChain(std::vector<T_Fragment> &fragments,
DNALength start, DNALength end,
std::vector<VectorIndex> &optFragmentChainIndices,
std::vector<T_Endpoint> *bufEndpointsPtr = NULL);
#include "GlobalChainImpl.hpp"
#endif
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