NCBI C++ ToolKit
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Blast wrappers for WindowMasker filtering. More...
#include <ncbi_pch.hpp>
#include "winmask_filter.hpp"
#include <sstream>
#include <serial/iterator.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objmgr/util/sequence.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/seqsrc_seqdb.hpp>
#include <algo/blast/api/local_blast.hpp>
#include <algo/blast/api/objmgr_query_data.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <algo/blast/api/windowmask_filter.hpp>
#include "blast_setup.hpp"
#include <algo/blast/core/blast_seqsrc.h>
#include <algo/blast/core/blast_hits.h>
#include <algo/blast/core/blast_filter.h>
#include <algo/blast/api/blast_aux.hpp>
#include <algo/winmask/seq_masker.hpp>
#include <corelib/env_reg.hpp>
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Functions | |
USING_SCOPE (objects) | |
static string | s_WINDOW_MASKER_STAT_FILE_NAME ("wmasker.obinary") |
static string | s_WINDOW_MASKER_PATH (kEmptyStr) |
DEFINE_STATIC_MUTEX (InitMutex) | |
int | WindowMaskerPathInit (const string &window_masker_path) |
Initialize the path to the windowmasker data files. More... | |
void | WindowMaskerPathReset () |
Resets the path to the windowmasker data files. More... | |
string | WindowMaskerPathGet () |
Retrieves the path to the windowmasker data files. More... | |
CSeqMasker * | s_BuildSeqMasker (const string &lstat) |
void | s_BuildMaskedRanges (CSeqMasker::TMaskList &masks, const CSeq_loc &seqloc, CSeq_id &query_id, TMaskedQueryRegions *mqr, CRef< CSeq_loc > *psl) |
template<class TQueries > | |
void | Blast_FindWindowMaskerLoc_Fwd (TQueries &query, const CBlastOptions *opts) |
template<class TQueries > | |
void | Blast_FindWindowMaskerLoc_Fwd (TQueries &query, const CBlastOptionsHandle *opts_handle) |
void | Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptions *opts_handle) |
Find Window Masker filtered locations using a BlastOptions. More... | |
void | Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptions *opts) |
Find Window Masker filtered locations using BlastOptions. More... | |
void | Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const CBlastOptionsHandle *opts_handle) |
Find Window Masker filtered locations using a BlastOptionsHandle. More... | |
void | Blast_FindWindowMaskerLoc (TSeqLocVector &query, const CBlastOptionsHandle *opts_handle) |
Find Window Masker filtered locations using a BlastOptionsHandle. More... | |
void | Blast_FindWindowMaskerLoc (CBlastQueryVector &query, const string &lstat) |
Find Window Masker filtered locations by database name. More... | |
void | Blast_FindWindowMaskerLoc (TSeqLocVector &query, const string &lstat) |
Find Window Masker filtered locations on TSeqLocVector by database name. More... | |
static string | s_FindPathToWM (void) |
Find the path to the window masker files, first checking the (optionally set) value passed to the WindowMaskerPathInit function, then the environment variable WINDOW_MASKER_PATH, then the section WINDOW_MASKER, label WINDOW_MASKER_PATH in the NCBI configuration file. More... | |
string | WindowMaskerTaxidToDb (const string &window_masker_path, int taxid) |
Get the windowmasker file path for a given taxid and base path. More... | |
string | WindowMaskerTaxidToDb (int taxid) |
Get the windowmasker file path for a given taxid. More... | |
void | Blast_FindWindowMaskerLocTaxId (CBlastQueryVector &query, int taxid) |
Find Window Masker filtered locations by taxonomic ID. More... | |
void | Blast_FindWindowMaskerLocTaxId (TSeqLocVector &query, int taxid) |
Find Window Masker filtered locations on a TSeqLocVector by Taxid. More... | |
static void | s_OldGetTaxIdWithWindowMaskerSupport (set< int > &supported_taxids) |
void | GetTaxIdWithWindowMaskerSupport (set< int > &supported_taxids) |
This function returns a list of NCBI taxonomy IDs for which there exists windowmasker masking data to support organism specific filtering. More... | |
Blast wrappers for WindowMasker filtering.
Definition in file winmask_filter.cpp.