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CWinMaskConfig Class Reference

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Objects of this class contain winmasker configuration data. More...

#include <algo/winmask/win_mask_config.hpp>

+ Collaboration diagram for CWinMaskConfig:

Classes

class  CIstreamProxy
 

Public Types

enum  EAppType {
  eAny , eComputeCounts , eConvertCounts , eGenerateMasks ,
  eGenerateMasksWithDuster
}
 
typedef CWinMaskUtil::CIdSet CIdSet
 
typedef CWinMaskUtil::CIdSet_SeqId CIdSet_SeqId
 
typedef CWinMaskUtil::CIdSet_TextMatch CIdSet_TextMatch
 

Public Member Functions

 CWinMaskConfig (const CArgs &args, EAppType type=eAny, bool determine_input=true)
 Object constructor. More...
 
 ~CWinMaskConfig ()
 Destructor. More...
 
CMaskReaderReader ()
 Get the input reader object. More...
 
CMaskWriterWriter ()
 Get the output writer object. More...
 
Uint4 Textend () const
 Get the t_extend value. More...
 
Uint4 CutoffScore () const
 Get the average unit score threshold. More...
 
Uint4 MaxScore () const
 Get the maximum unit score. More...
 
Uint4 MinScore () const
 Get the minimum unit score. More...
 
double MinScorePct () const
 
double ExtendScorePct () const
 
double ThresScorePct () const
 
double MaxScorePct () const
 
Uint4 SetMaxScore () const
 Get the alternative score for high scoring units. More...
 
Uint4 SetMinScore () const
 Get the alternative score for low scoring units. More...
 
Uint1 WindowSize () const
 Get the window size. More...
 
const string LStatName () const
 Get the name of the length statistics file. More...
 
bool MergePass () const
 Flag to run the interval merging passes. More...
 
Uint4 MergeCutoffScore () const
 Average unit score triggering the interval merging. More...
 
Uint4 AbsMergeCutoffDist () const
 Distance at which intervals are merged unconditionally. More...
 
Uint4 MeanMergeCutoffDist () const
 Distance at which intervals are considered candidates for merging. More...
 
const string Trigger () const
 Type of the event triggering the masking. More...
 
Uint1 TMin_Count () const
 Number of units to count. More...
 
bool Discontig () const
 Whether discontiguous units are used. More...
 
Uint4 Pattern () const
 Pattern to form discontiguous units. More...
 
Uint4 WindowStep () const
 Window step. More...
 
Uint1 UnitStep () const
 Unit step. More...
 
Uint1 MergeUnitStep () const
 Unit step to use for interval merging. More...
 
EAppType AppType () const
 Type of application to run. More...
 
bool FaList () const
 Use a list of fasta files. More...
 
Uint4 Mem () const
 Memory available for n-mer frequency counting. More...
 
Uint1 UnitSize () const
 n-mer size used for n-mer frequency counting. More...
 
Uint8 GenomeSize () const
 Total genome length. More...
 
string Input () const
 Value of the -input parameter. More...
 
string Output () const
 Value of the -output parameter. More...
 
string Th () const
 Percentage thresholds. More...
 
Uint4 DustWindow () const
 Dust window. More...
 
Uint4 DustLevel () const
 Dust level. More...
 
Uint4 DustLinker () const
 Dust linker (in bps). More...
 
bool CheckDup () const
 Check for possibly duplicate sequences in the input. More...
 
const string SFormat () const
 Format in which the unit counts generator should generate its output. More...
 
const string InFmt () const
 Input file format. More...
 
const CIdSetIds () const
 The set of query ids to process. More...
 
const CIdSetExcludeIds () const
 The set of query ids to exclude from processing. More...
 
bool UseBA () const
 Whether to use bit array optimization for optimized binary counts format. More...
 
bool MatchId () const
 Use CSeq_id objects to match/print sequence ids. More...
 
string const GetMetaData () const
 Get metadata string to be added to the counts file. More...
 

Static Public Member Functions

static void AddWinMaskArgs (CArgDescriptions &arg_desc, EAppType type=eAny, bool determine_input=true)
 

Private Member Functions

 CWinMaskConfig (const CWinMaskConfig &rhs)
 Prohibit copy constructor. More...
 
CWinMaskConfigoperator= (const CWinMaskConfig &rhs)
 Prohibit assignment operator. More...
 
CMaskWriterx_GetWriter (const CArgs &args)
 Create the CMaskWriter instance for this class. More...
 

Static Private Member Functions

static void FillIdList (const string &file_name, CIdSet &id_list)
 Read the list of sequence ids from a given file. More...
 
static EAppType s_DetermineAppType (const CArgs &args, EAppType user_specified_type)
 

Private Attributes

Window based masker configuration.
EAppType app_type
 type of application to run More...
 
CIstreamProxy is
 input file resource manager More...
 
CMaskReaderreader
 input reader object More...
 
CMaskWriterwriter
 output writer object More...
 
string lstat_name
 name of the file containing unit length statitsics More...
 
double t_low_pct
 minimum allowed unit score as percentage of units with lower count More...
 
double t_extend_pct
 minimum score for interval extension as percentage of units with lower count More...
 
double t_thres_pct
 threshold score for starting masking as percentage of units with lower count More...
 
double t_high_pct
 highest allowed unit score as percentage of units with lower count More...
 
Uint4 textend
 t_extend value for extension of masked intervals More...
 
Uint4 cutoff_score
 window score that triggers masking More...
 
Uint4 max_score
 maximum allowed unit score More...
 
Uint4 min_score
 minimum allowed unit score More...
 
Uint4 set_max_score
 score to use for high scoring units More...
 
Uint4 set_min_score
 score to use for low scoring units More...
 
Uint1 window_size
 length of a window in base pairs More...
 
bool merge_pass
 perform extra interval merging passes or not More...
 
Uint4 merge_cutoff_score
 average unit score triggering interval merging More...
 
Uint4 abs_merge_cutoff_dist
 distance triggering unconditional interval merging More...
 
Uint4 mean_merge_cutoff_dist
 distance at which intervals are considered for merging More...
 
string trigger
 type of the event that triggers masking More...
 
Uint1 tmin_count
 number of units to count for min trigger More...
 
bool discontig
 true, if using discontiguous units More...
 
Uint4 pattern
 base pattern to use for discontiguous units More...
 
Uint4 window_step
 window step More...
 
Uint1 unit_step
 unit step More...
 
Uint1 merge_unit_step
 unit step to use when merging intervals More...
 
bool fa_list
 indicates whether input is a list of fasta file names More...
 
Uint4 mem
 memory available for unit counts generator More...
 
Uint1 unit_size
 unit size (used in unit counts generator More...
 
Uint8 genome_size
 total size of the genome in bases More...
 
string input
 input file name More...
 
string output
 output file name (may be empty to indicate stdout) More...
 
string th
 percetages to compute winmask thresholds More...
 
Uint4 dust_window
 window size for dusting More...
 
Uint4 dust_level
 level value for dusting More...
 
Uint4 dust_linker
 number of bases to use for linking More...
 
bool checkdup
 check for duplicate contigs More...
 
string iformatstr
 input format More...
 
string sformat
 unit counts format for counts generator More...
 
Uint4 smem
 memory (in megabytes available for masking stage) More...
 
CIdSetids
 set of ids to process More...
 
CIdSetexclude_ids
 set of ids to exclude from processing More...
 
bool use_ba
 use bit array based optimization More...
 
bool text_match
 identify seq ids by string matching More...
 
string metadata
 metadata associated with counts file More...
 

Detailed Description

Objects of this class contain winmasker configuration data.

The class is also responsible for validation of command line arguments.

Definition at line 95 of file win_mask_config.hpp.

Member Typedef Documentation

◆ CIdSet

Definition at line 99 of file win_mask_config.hpp.

◆ CIdSet_SeqId

Definition at line 100 of file win_mask_config.hpp.

◆ CIdSet_TextMatch

Definition at line 101 of file win_mask_config.hpp.

Member Enumeration Documentation

◆ EAppType

Enumerator
eAny 
eComputeCounts 
eConvertCounts 
eGenerateMasks 
eGenerateMasksWithDuster 

Definition at line 103 of file win_mask_config.hpp.

Constructor & Destructor Documentation

◆ CWinMaskConfig() [1/2]

CWinMaskConfig::CWinMaskConfig ( const CArgs args,
EAppType  type = eAny,
bool  determine_input = true 
)

Object constructor.

Parameters
argsC++ toolkit style command line arguments.
typetype of application; eAny means application needs to be decided based on args
determine_inputwhen false, CWinMaskConfig is not concerned with the input files

Definition at line 319 of file win_mask_config.cpp.

References _TRACE, app_type, eComputeCounts, eConvertCounts, exclude_ids, CArgs::Exist(), FillIdList(), ids, iformatstr, is, kInput, kInputFormat, metadata, NCBI_THROW, reader, set_max_score, set_min_score, text_match, writer, and x_GetWriter().

◆ ~CWinMaskConfig()

CWinMaskConfig::~CWinMaskConfig ( )

Destructor.

Definition at line 448 of file win_mask_config.cpp.

References reader, and writer.

◆ CWinMaskConfig() [2/2]

CWinMaskConfig::CWinMaskConfig ( const CWinMaskConfig rhs)
private

Prohibit copy constructor.

Parameters
rhsobject to copy from [in]

Member Function Documentation

◆ AbsMergeCutoffDist()

Uint4 CWinMaskConfig::AbsMergeCutoffDist ( ) const
inline

Distance at which intervals are merged unconditionally.

Returns
The distance in base pairs such that if two consequtive masked intervals are closer to each other than that distance then they are merged unconditionally. This is the value of -mabs command line option to winmasker.

Definition at line 257 of file win_mask_config.hpp.

References abs_merge_cutoff_dist.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ AddWinMaskArgs()

void CWinMaskConfig::AddWinMaskArgs ( CArgDescriptions arg_desc,
EAppType  type = eAny,
bool  determine_input = true 
)
static

◆ AppType()

EAppType CWinMaskConfig::AppType ( ) const
inline

Type of application to run.

Returns
eComputeCounts to compute unit counts eConvertCounts to convert unit counts from one format to another eGenerateMasks to generate masks using only WindowMasker eGenerateMasks to generate masks using both WindowMasker and DustMasker

Definition at line 355 of file win_mask_config.hpp.

References app_type.

Referenced by CWinMaskApplication::Run().

◆ CheckDup()

bool CWinMaskConfig::CheckDup ( ) const
inline

Check for possibly duplicate sequences in the input.

Returns
true to check for duplicates; false otherwise

Definition at line 453 of file win_mask_config.hpp.

References checkdup.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ CutoffScore()

Uint4 CWinMaskConfig::CutoffScore ( ) const
inline

Get the average unit score threshold.

Returns
the current value of average unit score that triggers masking.

Definition at line 155 of file win_mask_config.hpp.

References cutoff_score.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ Discontig()

bool CWinMaskConfig::Discontig ( ) const
inline

Whether discontiguous units are used.

Returns
true if discontiguous units should be used; false otherwise

Definition at line 304 of file win_mask_config.hpp.

References discontig.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ DustLevel()

Uint4 CWinMaskConfig::DustLevel ( ) const
inline

Dust level.

Returns
dust level

Definition at line 436 of file win_mask_config.hpp.

References dust_level.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ DustLinker()

Uint4 CWinMaskConfig::DustLinker ( ) const
inline

Dust linker (in bps).

Returns
dust linker

Definition at line 444 of file win_mask_config.hpp.

References dust_linker.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ DustWindow()

Uint4 CWinMaskConfig::DustWindow ( ) const
inline

Dust window.

Returns
dust window

Definition at line 428 of file win_mask_config.hpp.

References dust_window.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ ExcludeIds()

const CIdSet* CWinMaskConfig::ExcludeIds ( ) const
inline

The set of query ids to exclude from processing.

The sequences from the input file that match this one of the ids in this list will be excluded from processing.

Returns
the set of query ids to exclude from processing

Definition at line 498 of file win_mask_config.hpp.

References exclude_ids.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ ExtendScorePct()

double CWinMaskConfig::ExtendScorePct ( ) const
inline

Definition at line 180 of file win_mask_config.hpp.

References t_extend_pct.

Referenced by CWinMaskApplication::Run().

◆ FaList()

bool CWinMaskConfig::FaList ( ) const
inline

Use a list of fasta files.

Returns
true indicates that -input parameter specifies a file containing a list of input fasta files; flase indicates that -input paramater specifies a single input fasta file

Definition at line 366 of file win_mask_config.hpp.

References fa_list.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ FillIdList()

void CWinMaskConfig::FillIdList ( const string file_name,
CIdSet id_list 
)
staticprivate

Read the list of sequence ids from a given file.

Parameters
file_namefile to read the ids from
id_listwhere to store the ids

Definition at line 467 of file win_mask_config.cpp.

References file, file_name, CWinMaskUtil::CIdSet::insert(), and NcbiGetlineEOL().

Referenced by CWinMaskConfig().

◆ GenomeSize()

Uint8 CWinMaskConfig::GenomeSize ( ) const
inline

Total genome length.

Returns
genome length as supplied on command line

Definition at line 388 of file win_mask_config.hpp.

References genome_size.

Referenced by CWinMaskApplication::Run().

◆ GetMetaData()

string const CWinMaskConfig::GetMetaData ( ) const
inline

Get metadata string to be added to the counts file.

Definition at line 515 of file win_mask_config.hpp.

References metadata.

Referenced by CWinMaskApplication::Run().

◆ Ids()

const CIdSet* CWinMaskConfig::Ids ( ) const
inline

The set of query ids to process.

Only the sequences from the input file that match one of the ids in this list will be processed.

Returns
the set of query ids to process

Definition at line 487 of file win_mask_config.hpp.

References ids.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ InFmt()

const string CWinMaskConfig::InFmt ( ) const
inline

Input file format.

Returns
string indicating input file format.

Definition at line 474 of file win_mask_config.hpp.

References iformatstr.

Referenced by CWinMaskApplication::Run().

◆ Input()

string CWinMaskConfig::Input ( ) const
inline

Value of the -input parameter.

Returns
value of the -input parameter.

Definition at line 396 of file win_mask_config.hpp.

References input.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ LStatName()

const string CWinMaskConfig::LStatName ( ) const
inline

Get the name of the length statistics file.

Returns
the name of the file containing the unit length statistics.

Definition at line 218 of file win_mask_config.hpp.

References lstat_name.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MatchId()

bool CWinMaskConfig::MatchId ( ) const
inline

Use CSeq_id objects to match/print sequence ids.

Returns
true if CSeq_id objects should be used; false if strings should be used

Definition at line 511 of file win_mask_config.hpp.

References text_match.

◆ MaxScore()

Uint4 CWinMaskConfig::MaxScore ( ) const
inline

Get the maximum unit score.

Returns
the current value of the maximum unit score. Any ecode with larger score will be assigned the score value specified by -setmaxscore command line option.

Definition at line 166 of file win_mask_config.hpp.

References max_score.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MaxScorePct()

double CWinMaskConfig::MaxScorePct ( ) const
inline

Definition at line 182 of file win_mask_config.hpp.

References t_high_pct.

Referenced by CWinMaskApplication::Run().

◆ MeanMergeCutoffDist()

Uint4 CWinMaskConfig::MeanMergeCutoffDist ( ) const
inline

Distance at which intervals are considered candidates for merging.

Returns
The distance in base pairs such that if two consequtive masked intervals are closer to each other tham that distance then they are considered candidates for merging. They have to pass mean average unit score test to be merged (see description of CWinMaskConfig::MergeCutoffScore()). This is the value of -mmean command line option to winmasker.

Definition at line 272 of file win_mask_config.hpp.

References mean_merge_cutoff_dist.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ Mem()

Uint4 CWinMaskConfig::Mem ( ) const
inline

Memory available for n-mer frequency counting.

Returns
memory in megabytes

Definition at line 374 of file win_mask_config.hpp.

References mem.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MergeCutoffScore()

Uint4 CWinMaskConfig::MergeCutoffScore ( ) const
inline

Average unit score triggering the interval merging.

For each pair of consequtive mask intervals winmasker that are candidates for merging (see description of CWinMaskConfig::MeanMergeCutoffDist()) winmasker evaluates the mean unit score of all units in the interval starting at the start of the first interval and ending at the end of the second interval. If the result is greater or equal than the value returned by this function the intervals are merged.

Returns
the value of the mean unit score triggering merging of masked intervals which is the value of -mscore command line option to winmasker.

Definition at line 246 of file win_mask_config.hpp.

References merge_cutoff_score.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MergePass()

bool CWinMaskConfig::MergePass ( ) const
inline

Flag to run the interval merging passes.

Returns
true if interval merging is requested, false otherwise.

Definition at line 227 of file win_mask_config.hpp.

References merge_pass.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MergeUnitStep()

Uint1 CWinMaskConfig::MergeUnitStep ( ) const
inline

Unit step to use for interval merging.

Returns
the distance between units used to estimate average unit score of the span of two intervals that are candidates for merging.

Definition at line 344 of file win_mask_config.hpp.

References merge_unit_step.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MinScore()

Uint4 CWinMaskConfig::MinScore ( ) const
inline

Get the minimum unit score.

Returns
the current value of the minimum unit score. Any ecode with smaller score will be assigned the score value specified by -setminscore command line option.

Definition at line 177 of file win_mask_config.hpp.

References min_score.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ MinScorePct()

double CWinMaskConfig::MinScorePct ( ) const
inline

Definition at line 179 of file win_mask_config.hpp.

References t_low_pct.

Referenced by CWinMaskApplication::Run().

◆ operator=()

CWinMaskConfig& CWinMaskConfig::operator= ( const CWinMaskConfig rhs)
private

Prohibit assignment operator.

Parameters
rhsobject to copy from [in]

◆ Output()

string CWinMaskConfig::Output ( ) const
inline

Value of the -output parameter.

Returns
value of the -output parameter.

Definition at line 404 of file win_mask_config.hpp.

References output.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ Pattern()

Uint4 CWinMaskConfig::Pattern ( ) const
inline

Pattern to form discontiguous units.

Pattern is a 4-byte long bit mask. Bit n is set to 1 iff the n-th base in a window should not be used in a pattern.

Returns
the base pattern to from discontiguous units

Definition at line 316 of file win_mask_config.hpp.

References pattern.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ Reader()

CMaskReader & CWinMaskConfig::Reader ( )

Get the input reader object.

Returns
the current input reader.

Definition at line 458 of file win_mask_config.cpp.

References NCBI_THROW, and reader.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ s_DetermineAppType()

CWinMaskConfig::EAppType CWinMaskConfig::s_DetermineAppType ( const CArgs args,
EAppType  user_specified_type 
)
staticprivate

◆ SetMaxScore()

Uint4 CWinMaskConfig::SetMaxScore ( ) const
inline

Get the alternative score for high scoring units.

Returns
the score value that is assigned to units that have original score larger than the value specified by -maxscore command line option.

Definition at line 192 of file win_mask_config.hpp.

References set_max_score.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ SetMinScore()

Uint4 CWinMaskConfig::SetMinScore ( ) const
inline

Get the alternative score for low scoring units.

Returns
the score value that is assigned to units that have original score smaller than the value specified by -minscore command line option.

Definition at line 202 of file win_mask_config.hpp.

References set_min_score.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ SFormat()

const string CWinMaskConfig::SFormat ( ) const
inline

Format in which the unit counts generator should generate its output.

Returns
unit counts file format

Definition at line 462 of file win_mask_config.hpp.

References r(), sformat, and smem.

Referenced by CWinMaskApplication::Run().

◆ Textend()

Uint4 CWinMaskConfig::Textend ( ) const
inline

Get the t_extend value.

Returns
the current t_extend value.

Definition at line 146 of file win_mask_config.hpp.

References textend.

Referenced by CWinMaskApplication::Run().

◆ Th()

string CWinMaskConfig::Th ( ) const
inline

Percentage thresholds.

Comma separated list of floating point numbers between 0.0 and 100.0 used to compute winmask score thresholds. The corresponding score thresholds will be added as comments to the end of the output. For each number the program finds the score such that the corresponding fraction of different n-mers has the lower score.

Returns
comma separated list of values

Definition at line 420 of file win_mask_config.hpp.

References th.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ ThresScorePct()

double CWinMaskConfig::ThresScorePct ( ) const
inline

Definition at line 181 of file win_mask_config.hpp.

References t_thres_pct.

Referenced by CWinMaskApplication::Run().

◆ TMin_Count()

Uint1 CWinMaskConfig::TMin_Count ( ) const
inline

Number of units to count.

If "-trigger min" was specified on the command line, then this parameter is the number of units that have to be above threshold to trigger masking.

Returns
number of units to count.

Definition at line 295 of file win_mask_config.hpp.

References tmin_count.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ Trigger()

const string CWinMaskConfig::Trigger ( ) const
inline

Type of the event triggering the masking.

Returns
string describing the type of the event that would trigger masking of a window. The allowed values are:
mean - average unit score exceeds the threshold;
min - minimum unit score exceeds the threshold.

Definition at line 283 of file win_mask_config.hpp.

References trigger.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ UnitSize()

Uint1 CWinMaskConfig::UnitSize ( ) const
inline

n-mer size used for n-mer frequency counting.

Returns
n-mer size in base pairs

Definition at line 382 of file win_mask_config.hpp.

References unit_size.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ UnitStep()

Uint1 CWinMaskConfig::UnitStep ( ) const
inline

Unit step.

Returns
the distance between consequtive units within a window

Definition at line 334 of file win_mask_config.hpp.

References unit_step.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ UseBA()

bool CWinMaskConfig::UseBA ( ) const
inline

Whether to use bit array optimization for optimized binary counts format.

Returns
true if optimization should be used; false otherwise

Definition at line 504 of file win_mask_config.hpp.

References use_ba.

Referenced by CWinMaskApplication::Run().

◆ WindowSize()

Uint1 CWinMaskConfig::WindowSize ( ) const
inline

Get the window size.

Returns
the current window size.

Definition at line 209 of file win_mask_config.hpp.

References window_size.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ WindowStep()

Uint4 CWinMaskConfig::WindowStep ( ) const
inline

Window step.

Returns
the number of bases between two consequtive windows

Definition at line 325 of file win_mask_config.hpp.

References window_step.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ Writer()

CMaskWriter& CWinMaskConfig::Writer ( )
inline

Get the output writer object.

Returns
the current output writer.

Definition at line 139 of file win_mask_config.hpp.

References writer.

Referenced by CWinMaskDemoApplication::Run(), and CWinMaskApplication::Run().

◆ x_GetWriter()

CMaskWriter * CWinMaskConfig::x_GetWriter ( const CArgs args)
private

Create the CMaskWriter instance for this class.

Parameters
argscommand line arguments
formatformat of the output to be written
Returns
writer based on the format requested
Exceptions
runtime_errorif the output format is not recognized

Definition at line 283 of file win_mask_config.cpp.

References BuildAlgorithmParametersString(), eBlast_filter_program_windowmasker, CArgValue::fBinary, format, kOutput, kOutputFormat, NULL, output, and NStr::StartsWith().

Referenced by CWinMaskConfig().

Member Data Documentation

◆ abs_merge_cutoff_dist

Uint4 CWinMaskConfig::abs_merge_cutoff_dist
private

distance triggering unconditional interval merging

Definition at line 646 of file win_mask_config.hpp.

Referenced by AbsMergeCutoffDist().

◆ app_type

EAppType CWinMaskConfig::app_type
private

type of application to run

Definition at line 628 of file win_mask_config.hpp.

Referenced by AppType(), and CWinMaskConfig().

◆ checkdup

bool CWinMaskConfig::checkdup
private

check for duplicate contigs

Definition at line 665 of file win_mask_config.hpp.

Referenced by CheckDup().

◆ cutoff_score

Uint4 CWinMaskConfig::cutoff_score
private

window score that triggers masking

Definition at line 638 of file win_mask_config.hpp.

Referenced by CutoffScore().

◆ discontig

bool CWinMaskConfig::discontig
private

true, if using discontiguous units

Definition at line 650 of file win_mask_config.hpp.

Referenced by Discontig().

◆ dust_level

Uint4 CWinMaskConfig::dust_level
private

level value for dusting

Definition at line 663 of file win_mask_config.hpp.

Referenced by DustLevel().

◆ dust_linker

Uint4 CWinMaskConfig::dust_linker
private

number of bases to use for linking

Definition at line 664 of file win_mask_config.hpp.

Referenced by DustLinker().

◆ dust_window

Uint4 CWinMaskConfig::dust_window
private

window size for dusting

Definition at line 662 of file win_mask_config.hpp.

Referenced by DustWindow().

◆ exclude_ids

CIdSet* CWinMaskConfig::exclude_ids
private

set of ids to exclude from processing

Definition at line 670 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), and ExcludeIds().

◆ fa_list

bool CWinMaskConfig::fa_list
private

indicates whether input is a list of fasta file names

Definition at line 655 of file win_mask_config.hpp.

Referenced by FaList().

◆ genome_size

Uint8 CWinMaskConfig::genome_size
private

total size of the genome in bases

Definition at line 658 of file win_mask_config.hpp.

Referenced by GenomeSize().

◆ ids

CIdSet* CWinMaskConfig::ids
private

set of ids to process

Definition at line 669 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), and Ids().

◆ iformatstr

string CWinMaskConfig::iformatstr
private

input format

Definition at line 666 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), and InFmt().

◆ input

string CWinMaskConfig::input
private

input file name

Definition at line 659 of file win_mask_config.hpp.

Referenced by Input().

◆ is

CIstreamProxy CWinMaskConfig::is
private

input file resource manager

Definition at line 629 of file win_mask_config.hpp.

Referenced by CWinMaskConfig().

◆ lstat_name

string CWinMaskConfig::lstat_name
private

name of the file containing unit length statitsics

Definition at line 632 of file win_mask_config.hpp.

Referenced by LStatName().

◆ max_score

Uint4 CWinMaskConfig::max_score
private

maximum allowed unit score

Definition at line 639 of file win_mask_config.hpp.

Referenced by MaxScore().

◆ mean_merge_cutoff_dist

Uint4 CWinMaskConfig::mean_merge_cutoff_dist
private

distance at which intervals are considered for merging

Definition at line 647 of file win_mask_config.hpp.

Referenced by MeanMergeCutoffDist().

◆ mem

Uint4 CWinMaskConfig::mem
private

memory available for unit counts generator

Definition at line 656 of file win_mask_config.hpp.

Referenced by Mem().

◆ merge_cutoff_score

Uint4 CWinMaskConfig::merge_cutoff_score
private

average unit score triggering interval merging

Definition at line 645 of file win_mask_config.hpp.

Referenced by MergeCutoffScore().

◆ merge_pass

bool CWinMaskConfig::merge_pass
private

perform extra interval merging passes or not

Definition at line 644 of file win_mask_config.hpp.

Referenced by MergePass().

◆ merge_unit_step

Uint1 CWinMaskConfig::merge_unit_step
private

unit step to use when merging intervals

Definition at line 654 of file win_mask_config.hpp.

Referenced by MergeUnitStep().

◆ metadata

string CWinMaskConfig::metadata
private

metadata associated with counts file

Definition at line 673 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), and GetMetaData().

◆ min_score

Uint4 CWinMaskConfig::min_score
private

minimum allowed unit score

Definition at line 640 of file win_mask_config.hpp.

Referenced by MinScore().

◆ output

string CWinMaskConfig::output
private

output file name (may be empty to indicate stdout)

Definition at line 660 of file win_mask_config.hpp.

Referenced by Output(), and x_GetWriter().

◆ pattern

Uint4 CWinMaskConfig::pattern
private

base pattern to use for discontiguous units

Definition at line 651 of file win_mask_config.hpp.

Referenced by Pattern().

◆ reader

CMaskReader* CWinMaskConfig::reader
private

input reader object

Definition at line 630 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), Reader(), and ~CWinMaskConfig().

◆ set_max_score

Uint4 CWinMaskConfig::set_max_score
private

score to use for high scoring units

Definition at line 641 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), and SetMaxScore().

◆ set_min_score

Uint4 CWinMaskConfig::set_min_score
private

score to use for low scoring units

Definition at line 642 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), and SetMinScore().

◆ sformat

string CWinMaskConfig::sformat
private

unit counts format for counts generator

Definition at line 667 of file win_mask_config.hpp.

Referenced by SFormat().

◆ smem

Uint4 CWinMaskConfig::smem
private

memory (in megabytes available for masking stage)

Definition at line 668 of file win_mask_config.hpp.

Referenced by SFormat().

◆ t_extend_pct

double CWinMaskConfig::t_extend_pct
private

minimum score for interval extension as percentage of units with lower count

Definition at line 634 of file win_mask_config.hpp.

Referenced by ExtendScorePct().

◆ t_high_pct

double CWinMaskConfig::t_high_pct
private

highest allowed unit score as percentage of units with lower count

Definition at line 636 of file win_mask_config.hpp.

Referenced by MaxScorePct().

◆ t_low_pct

double CWinMaskConfig::t_low_pct
private

minimum allowed unit score as percentage of units with lower count

Definition at line 633 of file win_mask_config.hpp.

Referenced by MinScorePct().

◆ t_thres_pct

double CWinMaskConfig::t_thres_pct
private

threshold score for starting masking as percentage of units with lower count

Definition at line 635 of file win_mask_config.hpp.

Referenced by ThresScorePct().

◆ text_match

bool CWinMaskConfig::text_match
private

identify seq ids by string matching

Definition at line 672 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), and MatchId().

◆ textend

Uint4 CWinMaskConfig::textend
private

t_extend value for extension of masked intervals

Definition at line 637 of file win_mask_config.hpp.

Referenced by Textend().

◆ th

string CWinMaskConfig::th
private

percetages to compute winmask thresholds

Definition at line 661 of file win_mask_config.hpp.

Referenced by Th().

◆ tmin_count

Uint1 CWinMaskConfig::tmin_count
private

number of units to count for min trigger

Definition at line 649 of file win_mask_config.hpp.

Referenced by TMin_Count().

◆ trigger

string CWinMaskConfig::trigger
private

type of the event that triggers masking

Definition at line 648 of file win_mask_config.hpp.

Referenced by Trigger().

◆ unit_size

Uint1 CWinMaskConfig::unit_size
private

unit size (used in unit counts generator

Definition at line 657 of file win_mask_config.hpp.

Referenced by UnitSize().

◆ unit_step

Uint1 CWinMaskConfig::unit_step
private

unit step

Definition at line 653 of file win_mask_config.hpp.

Referenced by UnitStep().

◆ use_ba

bool CWinMaskConfig::use_ba
private

use bit array based optimization

Definition at line 671 of file win_mask_config.hpp.

Referenced by UseBA().

◆ window_size

Uint1 CWinMaskConfig::window_size
private

length of a window in base pairs

Definition at line 643 of file win_mask_config.hpp.

Referenced by WindowSize().

◆ window_step

Uint4 CWinMaskConfig::window_step
private

window step

Definition at line 652 of file win_mask_config.hpp.

Referenced by WindowStep().

◆ writer

CMaskWriter* CWinMaskConfig::writer
private

output writer object

Definition at line 631 of file win_mask_config.hpp.

Referenced by CWinMaskConfig(), Writer(), and ~CWinMaskConfig().


The documentation for this class was generated from the following files:
Modified on Fri Apr 12 17:21:21 2024 by modify_doxy.py rev. 669887