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NCBI C++ ToolKit: CWinMaskCountsGenerator Class Reference

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This class encapsulates the n-mer frequency counts generation functionality of winmasker. More...

#include <algo/winmask/win_mask_gen_counts.hpp>

CWinMaskCountsGenerator (const string &input, const string &output, const string &infmt, const string &sformat, const string &th, Uint4 mem_avail, Uint1 unit_size, Uint8 genome_size, Uint4 min_count, Uint4 max_count, bool check_duplicates, bool use_list, const CWinMaskUtil::CIdSet *ids, const CWinMaskUtil::CIdSet *exclude_ids, bool use_ba, string const &metadata, double min_pct=-1.0, double extend_pct=-1.0, double thres_pct=-1.0, double max_pct=-1.0) Constructor. More...
CWinMaskCountsGenerator (const string &input, CNcbiOstream &os, const string &infmt, const string &sformat, const string &th, Uint4 mem_avail, Uint1 unit_size, Uint8 genome_size, Uint4 min_count, Uint4 max_count, bool check_duplicates, bool use_list, const CWinMaskUtil::CIdSet *ids, const CWinMaskUtil::CIdSet *exclude_ids, bool use_ba, string const &metadata, double min_pct=-1.0, double extend_pct=-1.0, double thres_pct=-1.0, double max_pct=-1.0) Constructor. More...
~CWinMaskCountsGenerator () Object destructor. More...
void operator() () This function does the actual n-mer counting. More...

This class encapsulates the n-mer frequency counts generation functionality of winmasker.

Definition at line 61 of file win_mask_gen_counts.hpp.

◆ CWinMaskCountsGenerator() [1/2] CWinMaskCountsGenerator::CWinMaskCountsGenerator ( const string & input, const string & output, const string & infmt, const string & sformat, const string & th, Uint4 mem_avail, Uint1 unit_size, Uint8 genome_size, Uint4 min_count, Uint4 max_count, bool check_duplicates, bool use_list, const CWinMaskUtil::CIdSet * ids, const CWinMaskUtil::CIdSet * exclude_ids, bool use_ba, string const & metadata, double min_pct = -1.0, double extend_pct = -1.0, double thres_pct = -1.0, double max_pct = -1.0 )

Constructor.

Creates an instance based on configuration parameters.

Parameters: input input file name or a name of the file containing a list of input files (one per line) depending on the value of use_list parameter output name of the output file (empty means standard output) infmt input format sformat counts format th string describing 4 percentage values (comma separated) used to compute winmask score thresholds mem_avail memory (in megabytes) available to the function unit_size n-mer size (value of n) min_count do not consider n-mers with counts less than the value this parameter max_count maximum n-mer count to consider in winmask thresholds computations check_duplicates true if input checking for duplicates is requested; false otherwise use_list true if input file contains the list of fasta file names; false if input is the name of the fasta file itself ids set of ids to consider exclude_ids set of ids to ignore use_ba use bit array optimization for optimized binary unit counts format metadata the metadata string min_pct min score as percentage of counts extend_pct interval extension score as percentage of counts thres_pct masking threshold score as percentage of counts max_pct max score as percentage of counts

Definition at line 171 of file win_mask_gen_counts.cpp.

References count, and th.

◆ CWinMaskCountsGenerator() [2/2] CWinMaskCountsGenerator::CWinMaskCountsGenerator ( const string & input, CNcbiOstream & os, const string & infmt, const string & sformat, const string & th, Uint4 mem_avail, Uint1 unit_size, Uint8 genome_size, Uint4 min_count, Uint4 max_count, bool check_duplicates, bool use_list, const CWinMaskUtil::CIdSet * ids, const CWinMaskUtil::CIdSet * exclude_ids, bool use_ba, string const & metadata, double min_pct = -1.0, double extend_pct = -1.0, double thres_pct = -1.0, double max_pct = -1.0 )

Constructor.

Creates an instance based on configuration parameters.

Parameters: input input file name or a name of the file containing a list of input files (one per line) depending on the value of use_list parameter os the output stream infmt input format sformat counts format th string describing 4 percentage values (comma separated) used to compute winmask score thresholds mem_avail memory (in megabytes) available to the function unit_size n-mer size (value of n) min_count do not consider n-mers with counts less than the value this parameter max_count maximum n-mer count to consider in winmask thresholds computations check_duplicates true if input checking for duplicates is requested; false otherwise use_list true if input file contains the list of fasta file names; false if input is the name of the fasta file itself ids set of ids to consider exclude_ids set of ids to ignore use_ba use bit array optimization for optimized binary unit counts format metadata the metadata string min_pct min score as percentage of counts extend_pct interval extension score as percentage of counts thres_pct masking threshold score as percentage of counts max_pct max score as percentage of counts

Definition at line 124 of file win_mask_gen_counts.cpp.

References count, and th.

◆ ~CWinMaskCountsGenerator() CWinMaskCountsGenerator::~CWinMaskCountsGenerator ( ) ◆ fastalen() ◆ operator()() void CWinMaskCountsGenerator::operator() ( void )

This function does the actual n-mer counting.

Determines the prefix length based on the available memory and calls process for each prefix to compute partial counts.

Definition at line 226 of file win_mask_gen_counts.cpp.

References _TRACE, check_duplicates, CheckDuplicates(), exclude_ids, fastalen(), CSeqMaskerOstat::finalize(), genome_size, has_min_count, i, ids, infmt, input, LOG_POST, max_count, max_mem, min_count, NCBI_ASSERT, NCBI_THROW, no_extra_pass, offset, process(), score_counts, CSeqMaskerOstat::setComment(), CSeqMaskerOstat::SetCount(), CSeqMaskerOstat::SetMaxCount(), CSeqMaskerOstat::setParam(), CSeqMaskerOstat::setUnitSize(), NStr::Split(), t_high, th, total_ecodes, unit_size, use_list, and ustat.

◆ process()

Definition at line 409 of file win_mask_gen_counts.cpp.

References _TRACE, ambig(), CWinMaskUtil::consider(), count, data, CBioseq_Handle::eCoding_Iupac, exclude_ids, CObjectManager::GetInstance(), i, ids, infmt, letter(), max_count, min_count, om, reverse_complement(), score_counts, CSeqMaskerOstat::setUnitCount(), t_high, total_ecodes, unit_size, and ustat.

Referenced by operator()().

◆ check_duplicates bool CWinMaskCountsGenerator::check_duplicates private ◆ exclude_ids ◆ genome_size Uint8 CWinMaskCountsGenerator::genome_size private ◆ has_min_count bool CWinMaskCountsGenerator::has_min_count private ◆ ids ◆ infmt string CWinMaskCountsGenerator::infmt private ◆ input string CWinMaskCountsGenerator::input private ◆ max_count Uint4 CWinMaskCountsGenerator::max_count private ◆ max_mem Uint8 CWinMaskCountsGenerator::max_mem private ◆ min_count Uint4 CWinMaskCountsGenerator::min_count private ◆ no_extra_pass bool CWinMaskCountsGenerator::no_extra_pass private ◆ score_counts vector< Uint4 > CWinMaskCountsGenerator::score_counts private ◆ t_high Uint4 CWinMaskCountsGenerator::t_high private ◆ th double CWinMaskCountsGenerator::th[4] private ◆ total_ecodes Uint4 CWinMaskCountsGenerator::total_ecodes private ◆ unit_size Uint4 CWinMaskCountsGenerator::unit_size private ◆ use_list bool CWinMaskCountsGenerator::use_list private ◆ ustat

The documentation for this class was generated from the following files:

include/algo/winmask/win_mask_gen_counts.hpp
src/algo/winmask/win_mask_gen_counts.cpp

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