NCBI C++ ToolKit
Functions
dust_filter.cpp File Reference

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>
+ Include dependency graph for dust_filter.cpp:

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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_Mappers_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...
 

Detailed Description

Calls sym dust lib in algo/dustmask and returns CSeq_locs for use by BLAST.

Definition in file dust_filter.cpp.

Modified on Mon Feb 26 03:59:39 2024 by modify_doxy.py rev. 669887