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NCBI C++ ToolKit: include/algo/winmask/win_mask_config.hpp Source File

eGenerateMasksWithDuster

()

{

trigger; }

()

{

; }

<< sformat << smem;

()

{

use_ba; }

EAppType

= eAny,

determine_input =

);

: resource( newResource ) {}

{

( resource && resource != &

)

resource; }

()

{

resource !=

; }

FillIdList(

&

,

Virtual base class for all input readers.

A base class for winmasker output writers.

Winmasker configuration errors.

virtual const char * GetErrCodeString() const override

Get the description of an error.

NCBI_EXCEPTION_DEFAULT(CWinMaskConfigException, CException)

@ eInconsistentOptions

Option validation failure.

@ eInputOpenFail

Can not open input file.

@ eReaderAllocFail

Memory allocation for input reader object failed.

const CNcbiIstream * operator->() const

CNcbiIstream * operator->()

CIstreamProxy(CNcbiIstream *newResource=NULL)

const CNcbiIstream & operator*() const

CNcbiIstream & operator*()

Objects of this class contain winmasker configuration data.

string trigger

type of the event that triggers masking

Uint4 merge_cutoff_score

average unit score triggering interval merging

string iformatstr

input format

Uint4 dust_level

level value for dusting

string Th() const

Percentage thresholds.

bool merge_pass

perform extra interval merging passes or not

double MinScorePct() const

double t_low_pct

minimum allowed unit score as percentage of units with lower count

Uint4 MeanMergeCutoffDist() const

Distance at which intervals are considered candidates for merging.

const CIdSet * ExcludeIds() const

The set of query ids to exclude from processing.

CMaskWriter * writer

output writer object

CMaskReader * reader

input reader object

Uint4 smem

memory (in megabytes available for masking stage)

Uint1 TMin_Count() const

Number of units to count.

bool MergePass() const

Flag to run the interval merging passes.

bool FaList() const

Use a list of fasta files.

CWinMaskUtil::CIdSet CIdSet

Uint4 pattern

base pattern to use for discontiguous units

Uint4 min_score

minimum allowed unit score

double MaxScorePct() const

const CIdSet * Ids() const

The set of query ids to process.

Uint1 merge_unit_step

unit step to use when merging intervals

bool CheckDup() const

Check for possibly duplicate sequences in the input.

bool use_ba

use bit array based optimization

Uint1 UnitStep() const

Unit step.

Uint4 SetMinScore() const

Get the alternative score for low scoring units.

bool UseBA() const

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

CWinMaskConfig(const CWinMaskConfig &rhs)

Prohibit copy constructor.

string Input() const

Value of the -input parameter.

const string InFmt() const

Input file format.

bool fa_list

indicates whether input is a list of fasta file names

double t_extend_pct

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

Uint1 tmin_count

number of units to count for min trigger

bool discontig

true, if using discontiguous units

Uint1 UnitSize() const

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

Uint4 DustLinker() const

Dust linker (in bps).

double ExtendScorePct() const

const string Trigger() const

Type of the event triggering the masking.

Uint4 mem

memory available for unit counts generator

Uint8 genome_size

total size of the genome in bases

EAppType AppType() const

Type of application to run.

CWinMaskConfig & operator=(const CWinMaskConfig &rhs)

Prohibit assignment operator.

CIstreamProxy is

input file resource manager

Uint4 WindowStep() const

Window step.

Uint4 mean_merge_cutoff_dist

distance at which intervals are considered for merging

string Output() const

Value of the -output parameter.

string output

output file name (may be empty to indicate stdout)

CIdSet * exclude_ids

set of ids to exclude from processing

string sformat

unit counts format for counts generator

CWinMaskUtil::CIdSet_TextMatch CIdSet_TextMatch

Uint4 cutoff_score

window score that triggers masking

bool MatchId() const

Use CSeq_id objects to match/print sequence ids.

Uint4 window_step

window step

EAppType app_type

type of application to run

Uint4 DustWindow() const

Dust window.

const string LStatName() const

Get the name of the length statistics file.

string const GetMetaData() const

Get metadata string to be added to the counts file.

Uint4 set_max_score

score to use for high scoring units

const string SFormat() const

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

Uint4 textend

t_extend value for extension of masked intervals

Uint4 Mem() const

Memory available for n-mer frequency counting.

Uint4 Textend() const

Get the t_extend value.

string metadata

metadata associated with counts file

Uint4 max_score

maximum allowed unit score

string input

input file name

bool Discontig() const

Whether discontiguous units are used.

double t_thres_pct

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

Uint1 unit_size

unit size (used in unit counts generator

Uint4 DustLevel() const

Dust level.

CIdSet * ids

set of ids to process

Uint4 MaxScore() const

Get the maximum unit score.

Uint4 SetMaxScore() const

Get the alternative score for high scoring units.

Uint4 Pattern() const

Pattern to form discontiguous units.

Uint4 dust_linker

number of bases to use for linking

Uint8 GenomeSize() const

Total genome length.

Uint4 MergeCutoffScore() const

Average unit score triggering the interval merging.

Uint1 unit_step

unit step

Uint4 dust_window

window size for dusting

Uint4 abs_merge_cutoff_dist

distance triggering unconditional interval merging

bool text_match

identify seq ids by string matching

Uint4 set_min_score

score to use for low scoring units

string lstat_name

name of the file containing unit length statitsics

Uint4 MinScore() const

Get the minimum unit score.

double ThresScorePct() const

Uint4 AbsMergeCutoffDist() const

Distance at which intervals are merged unconditionally.

string th

percetages to compute winmask thresholds

CWinMaskUtil::CIdSet_SeqId CIdSet_SeqId

Uint4 CutoffScore() const

Get the average unit score threshold.

Uint1 window_size

length of a window in base pairs

CMaskWriter & Writer()

Get the output writer object.

Uint1 MergeUnitStep() const

Unit step to use for interval merging.

bool checkdup

check for duplicate contigs

Uint1 WindowSize() const

Get the window size.

double t_high_pct

highest allowed unit score as percentage of units with lower count

Implementation of CIdSet that compares CSeq_id handles.

Implementation of CIdSet that does substring matching.

Base class for sets of seq_id representations used with -ids and -exclude-ids options.

The NCBI C++ standard methods for dealing with std::string.

static SQLCHAR output[256]

uint8_t Uint1

1-byte (8-bit) unsigned integer

uint32_t Uint4

4-byte (32-bit) unsigned integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

#define NCBI_XALGOWINMASK_EXPORT

<!DOCTYPE HTML >< html > n< header > n< title > PubSeq Gateway Help Page</title > n< style > n th

GenericReader< UTF8< char >, UTF8< char >, CrtAllocator > Reader

Reader with UTF8 encoding and default allocator.

Defines command line argument related classes.

NCBI C++ stream class wrappers for triggering between "new" and "old" C++ stream libraries.

double r(size_t dimension_, const Int4 *score_, const double *prob_, double theta_)

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