NCBI C++ ToolKit
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Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST. More...
#include <ncbi_pch.hpp>
#include "dust_filter.hpp"
#include <serial/iterator.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objmgr/util/sequence.hpp>
#include <objmgr/seq_loc_mapper.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <objmgr/seq_vector.hpp>
#include <algo/dustmask/symdust.hpp>
#include <string.h>
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Functions | |
USING_SCOPE (objects) | |
void | Blast_FindDustFilterLoc (TSeqLocVector &query, const CBlastNucleotideOptionsHandle *nucl_handle) |
Finds dust locations for a given set of sequences by calling the the symmetric dust lib. More... | |
static CRef< CSeq_loc_Mapper > | s_CreateSeqLocMapper (CSeq_id &query_id, const CSeq_loc *target_seqloc, CScope *scope) |
Auxiliary function to create CSeq_loc_Mapper from a copy of the target Seq-loc. More... | |
void | s_CombineDustMasksWithUserProvidedMasks (CSeqVector &data, CConstRef< CSeq_loc > seqloc, CRef< CScope > scope, CRef< CSeq_id > query_id, CRef< CSeq_loc > &orig_query_mask, Uint4 level, Uint4 window, Uint4 linker) |
void | Blast_FindDustFilterLoc (TSeqLocVector &query, Uint4 level=CSymDustMasker::DEFAULT_LEVEL, Uint4 window=CSymDustMasker::DEFAULT_WINDOW, Uint4 linker=CSymDustMasker::DEFAULT_LINKER) |
Overloaded version of the function above which takes the filtering implementation's arguments directly, TSeqLocVector version. More... | |
void | Blast_FindDustFilterLoc (CBlastQueryVector &query, Uint4 level=CSymDustMasker::DEFAULT_LEVEL, Uint4 window=CSymDustMasker::DEFAULT_WINDOW, Uint4 linker=CSymDustMasker::DEFAULT_LINKER) |
Overloaded version of the function above which takes the filtering implementation's arguments directly, CBlastQueryVector version. More... | |
Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.
Definition in file dust_filter.cpp.