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NCBI C++ ToolKit: src/algo/winmask/win_mask_config.cpp Source File

59 "file with unit counts"

62

arg_desc.

AddKey

(

"ustat"

"unit_counts"

63 "file with unit counts"

68 "(not optional if used with -mk_counts or -convert options)"

75 "check for duplicate sequences"

79 "indicates that -input represents a file containing " 80 "a list of names of fasta files to process, one name " 84 "memory available for mk_counts option in megabytes"

87 "add metadata to the counts file"

90 "number of bases in a unit"

93 "total size of the genome"

99

arg_desc.

AddOptionalKey

(

"window"

"window_size"

"window size"

102 "window score above which it is allowed to extend masking"

105 "window score threshold used to trigger masking"

108 "alternative high score for a unit if the" 109 "original unit score is more than highscore"

112 "alternative low score for a unit if the" 113 "original unit score is lower than lowscore"

125

arg_desc.

AddFlag

(

"parse_seqids"

126 "Parse Seq-ids in FASTA input"

true

);

128 "controls the format of the masker output (for masking stage only)"

138 "maximum useful unit score"

141 "maximum useful unit score as percentage"

144 "window score threshold used to trigger masking as percentage"

147 "window score above which it is allowed to extend masking as percentage"

150 "minimum useful unit score"

153 "minimum useful unit score as percentage"

168 "controls the format of the masker input"

170

arg_desc.

AddDefaultKey

(

"exclude_ids"

"exclude_id_list"

171 "file containing the list of ids to exclude from processing"

174 "file containing the list of ids to process"

177 "match ids as strings"

183

strings_allowed->

Allow

(

"seqids"

);

188 "controls the format of the output file containing the unit counts " 189 "(for counts generation and conversion only)"

196

->Allow(

"obinary"

) );

198 "target size of the output file containing the unit counts"

203 "combine window masking with dusting"

206 "dust minimum level"

211

arg_desc.

AddFlag

(

"mk_counts"

"generate frequency counts for a database"

);

212

arg_desc.

AddFlag

(

"convert"

"convert counts between different formats"

);

264 if

(args[

"mk_counts"

])

266 else if

(args[

"convert"

])

268 else if

(args[

"ustat"

])

272 "one of '-mk_counts', '-convert' or '-ustat <stat_file>' " 273 "must be specified"

);

288 if

(

format

"interval"

) {

291

}

else if

(

format

"fasta"

) {

313 throw

runtime_error(

"Unknown output format"

);

320

: app_type(s_DetermineAppType(args,

type

)),

321

is( app_type >= eGenerateMasks && args[

kInputFormat

].AsString() !=

"blastdb" 323

( !(args[

kInput

].AsString() ==

"-"

)

326

lstat_name( app_type >= eGenerateMasks ? args[

"ustat"

].AsString() :

""

327

t_low_pct( app_type != eConvertCounts && args[

"t_low_pct"

] ? args[

"t_low_pct"

].AsDouble() : -1.0 ),

328

t_extend_pct( app_type != eConvertCounts && args[

"t_extend_pct"

] ? args[

"t_extend_pct"

].AsDouble() : -1.0 ),

329

t_thres_pct( app_type != eConvertCounts && args[

"t_thres_pct"

] ? args[

"t_thres_pct"

].AsDouble() : -1.0 ),

330

t_high_pct( app_type != eConvertCounts && args[

"t_high_pct"

] ? args[

"t_high_pct"

].AsDouble() : -1.0 ),

331

textend( app_type >= eGenerateMasks && args[

"t_extend"

] ? args[

"t_extend"

].AsInteger() : 0 ),

332

cutoff_score( app_type >= eGenerateMasks && args[

"t_thres"

] ? args[

"t_thres"

].AsInteger() : 0 ),

333

max_score( app_type != eConvertCounts && args[

"t_high"

] ? args[

"t_high"

].AsInteger() : 0 ),

334

min_score( app_type != eConvertCounts && args[

"t_low"

] ? args[

"t_low"

].AsInteger() : 0 ),

335 window_size

( app_type >= eGenerateMasks && args[

"window"

] ? args[

"window"

].AsInteger() : 0 ),

337

merge_cutoff_score( 50 ),

338

abs_merge_cutoff_dist( 8 ),

339

mean_merge_cutoff_dist( 50 ),

346

merge_unit_step( 1 ),

347

fa_list( app_type == eComputeCounts && determine_input ? args[

"fa_list"

].AsBoolean() :

false

348

mem( app_type == eComputeCounts ? args[

"mem"

].AsInteger() : 0 ),

349

unit_size( app_type == eComputeCounts && args[

"unit"

] ? args[

"unit"

].AsInteger() : 0 ),

350

genome_size( app_type == eComputeCounts && args[

"genome_size"

] ? args[

"genome_size"

].AsInt8() : 0 ),

351 input

( determine_input ? args[

kInput

].AsString() :

""

353 th

(

"90,99,99.5,99.8"

355

dust_level( app_type == eGenerateMasksWithDuster ? args[

"dust_level"

].AsInteger() : 0 ),

357

checkdup( app_type == eComputeCounts ? args[

"checkdup"

].AsBoolean() :

false

358

sformat( app_type < eGenerateMasks ? args[

"sformat"

].AsString() :

""

359

smem( app_type < eGenerateMasks ? args[

"smem"

].AsInteger() : 0 ),

360

ids( 0 ), exclude_ids( 0 ),

361

use_ba( app_type != eConvertCounts ),

362

text_match( app_type != eConvertCounts && args[

"text_match"

].AsBoolean() )

364 if

(args.

Exist

(

"meta"

) && args[

"meta"

]) {

365 metadata

= args[

"meta"

].AsString();

367 _TRACE

(

"Entering CWinMaskConfig::CWinMaskConfig()"

);

381

args[

kInput

].AsString() );

384 if

(determine_input &&

iformatstr

"seqids"

){

393

eReaderAllocFail,

""

);

399 set_max_score

= args[

"set_t_high"

] ? args[

"set_t_high"

].AsInteger()

401 set_min_score

= args[

"set_t_low"

] ? args[

"set_t_low"

].AsInteger()

405 string

ids_file_name( args[

"ids"

].AsString() );

406 string

exclude_ids_file_name( args[

"exclude_ids"

].AsString() );

408 if

( !ids_file_name.empty()

409

&& !exclude_ids_file_name.empty() )

412 "only one of -ids or -exclude_ids can be specified"

);

415 if

( !ids_file_name.empty() ) {

423 "-text_match false can be used only with " 430 if

( !exclude_ids_file_name.empty() ) {

438 "-text_match false can be used only with " 445 _TRACE

(

"Leaving CWinMaskConfig::CWinMaskConfig"

);

461 "User options caused reader not to be created; can't get reader"

);

476

string::size_type stop( line.find_first_of(

" \t"

) );

477

string::size_type start( line[0] ==

'>'

? 1 : 0 );

478 string

id_str = line.substr( start, stop - start );

479

id_list.

insert

( id_str );

491 return "can not open input stream"

;

495 return "can not allocate fasta sequence reader"

;

499 return "inconsistent program options"

;

Class for reading sequences from BLAST databases.

Class for reading sequences from fasta files.

Virtual base class for all input readers.

Output filter to print masked sequence locations as Blast-db-mask-info objects.

Output filter to write masked data in fasta format.

Output filter to print masked sequences as sets of intervals.

Output filter to print masked sequence locations as NCBI Seq-loc objects.

A base class for winmasker output writers.

Winmasker configuration errors.

virtual const char * GetErrCodeString() const override

Get the description of an error.

@ eInconsistentOptions

Option validation failure.

@ eInputOpenFail

Can not open input file.

@ eReaderAllocFail

Memory allocation for input reader object failed.

string iformatstr

input format

static void FillIdList(const string &file_name, CIdSet &id_list)

Read the list of sequence ids from a given file.

CMaskWriter * writer

output writer object

CMaskReader * reader

input reader object

@ eGenerateMasksWithDuster

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

Object constructor.

CIstreamProxy is

input file resource manager

CMaskWriter * x_GetWriter(const CArgs &args)

Create the CMaskWriter instance for this class.

string output

output file name (may be empty to indicate stdout)

CIdSet * exclude_ids

set of ids to exclude from processing

CWinMaskUtil::CIdSet_TextMatch CIdSet_TextMatch

EAppType app_type

type of application to run

CMaskReader & Reader()

Get the input reader object.

Uint4 set_max_score

score to use for high scoring units

string metadata

metadata associated with counts file

~CWinMaskConfig()

Destructor.

CIdSet * ids

set of ids to process

bool text_match

identify seq ids by string matching

Uint4 set_min_score

score to use for low scoring units

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

CWinMaskUtil::CIdSet_SeqId CIdSet_SeqId

static EAppType s_DetermineAppType(const CArgs &args, EAppType user_specified_type)

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

virtual void insert(const string &id_str)=0

Add a string to the id set.

static SQLCHAR output[256]

void AddFlag(const string &name, const string &comment, CBoolEnum< EFlagValue > set_value=eFlagHasValueIfSet, TFlags flags=0)

Add description for flag argument.

void SetConstraint(const string &name, const CArgAllow *constraint, EConstraintNegate negate=eConstraint)

Set additional user defined constraint on argument value.

bool Exist(const string &name) const

Check existence of argument description.

void AddKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for mandatory key.

void AddOptionalKey(const string &name, const string &synopsis, const string &comment, EType type, TFlags flags=0)

Add description for optional key without default value.

CArgAllow_Strings * Allow(const string &value)

Add allowed string values.

void SetCurrentGroup(const string &group)

Set current arguments group name.

void AddDefaultKey(const string &name, const string &synopsis, const string &comment, EType type, const string &default_value, TFlags flags=0, const string &env_var=kEmptyStr, const char *display_value=nullptr)

Add description for optional key with default value.

@ eExcludes

One argument excludes another.

@ eInputFile

Name of file (must exist and be readable)

@ eBoolean

{'true', 't', 'false', 'f'}, case-insensitive

@ eDouble

Convertible into a floating point number (double)

@ eString

An arbitrary string.

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

@ fBinary

Open file in binary mode.

TErrCode GetErrCode(void) const

Get error code.

#define NCBI_THROW(exception_class, err_code, message)

Generic macro to throw an exception, given the exception class, error code and message string.

virtual const char * GetErrCodeString(void) const

Get error code interpreted as text.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

CNcbiIstream & NcbiGetlineEOL(CNcbiIstream &is, string &str, string::size_type *count=NULL)

Read from "is" to "str" the next line (taking into account platform specifics of End-of-Line)

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::ifstream CNcbiIfstream

Portable alias for ifstream.

static bool StartsWith(const CTempString str, const CTempString start, ECase use_case=eCase)

Check if a string starts with a specified prefix value.

@ eBlast_filter_program_windowmasker

The blob sat and sat key Both must be positive integers</td > n< td > Non empty string The interpretation of the blob id depends on a processor Cassandra n processor expects the following format

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

Contains the command line options common to filtering algorithms.

const size_t kNumInputFormats

Number of elements in kInputFormats.

const char * kOutputFormats[]

Output formats allowed, the first one is the default.

const size_t kNumOutputFormats

Number of elements in kOutputFormats.

const std::string kOutput

Command line flag to specify the output.

const std::string kOutputFormat

Command line flag to specify the output format.

const char * kInputFormats[]

Input formats allowed, the first one is the default.

const std::string kInput

Command line flag to specify the input.

const std::string kInputFormat

Command line flag to specify the input format.

string BuildAlgorithmParametersString(const CArgs &args)

Builds an algorithm options string for the filtering applications (segmasker, dustmasker) by examinin...

NCBI C++ auxiliary debug macros.

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Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Showing content from http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/doxyhtml/win__mask__config_8cpp_source.html below:

NCBI C++ ToolKit: src/algo/winmask/win_mask_config.cpp Source File

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