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NCBI C++ ToolKit: src/algo/blast/blastinput/magicblast_args.cpp Source File

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Declares the BLAST exception class.

Interface for reading SRA sequences into blast input.

Auxiliary classes/functions for BLAST input library.

int GetQueryBatchSize(EProgram program, bool is_ungapped=false, bool remote=false, bool use_default=true, string task="", bool mt_mode=false)

Retrieve the appropriate batch size for the specified task.

#define BLAST_WORDSIZE_MAPPER

default word size for mapping rna-seq to a genome

@ eMapper

Jumper alignment for mapping.

Class to constrain the values of an argument to those greater than or equal to the value specified in...

Class to constrain the values of an argument to those less than or equal to the value specified in th...

CRef< CRemoteArgs > m_RemoteArgs

remote vs. local execution options

CRef< CQueryOptionsArgs > m_QueryOptsArgs

query options object

CRef< CBlastDatabaseArgs > m_BlastDbArgs

database/subject object

CRef< CDebugArgs > m_DebugArgs

Debugging arguments.

CRef< CMTArgs > m_MTArgs

multi-threaded options

CRef< CFormattingArgs > m_FormattingArgs

formatting options

TBlastCmdLineArgs m_Args

Set of command line argument objects.

CRef< CStdCmdLineArgs > m_StdCmdLineArgs

standard command line arguments class

Argument class to collect database/subject arguments.

void SetDatabaseMaskingSupport(bool val)

Turns on/off database masking support.

Encapsulates ALL the BLAST algorithm's options.

EAPILocality

Enumerates the possible contexts in which objects of this type can be used.

Argument class to collect debugging options.

Argument class to collect formatting options, use this to create a CBlastFormat object.

Argument class for general search BLAST algorithm options: evalue, gap penalties, query filter string...

Argument class for collecting the largest intron size.

Argument class to collect multi-threaded arguments.

size_t m_NumThreads

Number of threads to spawn.

CMagicBlastAppArgs()

Constructor.

virtual CRef< CBlastOptionsHandle > x_CreateOptionsHandle(CBlastOptions::EAPILocality locality, const CArgs &args)

@inheritDoc

virtual int GetQueryBatchSize() const

@inheritDoc

Handle to the nucleotide mapping options to the BLAST algorithm.

Formatting args for magicblast advertising only SAM and fast tabular formats.

Special generic search arguments for blastmapper.

CMapperGenericSearchArgs(void)

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

Longest intron size with non-zero defalut value.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

MT args that allow multiple threads with a FASTA subject.

virtual void ExtractAlgorithmOptions(const CArgs &args, CBlastOptions &)

Interface method,.

Nucleotide args with no reward score.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

Program description without BLAST+ version.

CMapperProgramDescriptionArgs(const string &program_name, const string &program_desc)

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

Argument class to collect query options for BLAST Mapper.

RemoteArgs with no option for remote.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

StdCmdLineArgs with output stream for unaligned reads.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

CMapperStdCmdLineArgs(void)

Defines values for match and mismatch in nucleotide comparisons as well as non-greedy extension.

Argument class to populate an application's name and description.

string m_ProgDesc

Application's description.

string m_ProgName

Application's name.

Argument class to collect remote vs. local execution.

bool ExecuteRemotely() const

Return whether the search should be executed remotely or not.

Argument class to retrieve input and output streams for a command line program.

virtual void SetArgumentDescriptions(CArgDescriptions &arg_desc)

Interface method,.

void SetGzipEnabled(bool g)

Set automatic decompression of the input file is file name is recognized.

static unsigned int GetCpuCount(void)

Return number of active CPUs/cores (never less than 1).

const string kArgRevFwd

Argument to specify reverse/forward strand specificity.

const string kArgMaxIntronLength

Argument to specify the maximum length of an intron when linking multiple distinct alignments (applic...

const string kArgPercentIdentity

Argument to specify the target percent identity.

const string kArgGapExtend

Argument to select the gap extending penalty.

const string kArgUnalignedOutput

Argument to output unaligned reads in a separate file.

const string kArgGapOpen

Argument to select the gap opening penalty.

const string kArgMismatch

Argument to select the nucleotide mismatch penalty.

const string kArgFwdRev

Argument to specify forward/reverse strand specificity.

const string kArgNoUnaligned

Argument to trun off printing of unaligned reads.

const string kArgWordSize

Argument to select the wordfinder's word size.

const string kArgNumThreads

Argument to determine the number of threads to use when running BLAST.

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.

void SetDependency(const string &arg1, EDependency dep, const string &arg2)

Define a dependency.

bool Exist(const string &name) const

Check existence of argument description.

void SetUsageContext(const string &usage_name, const string &usage_description, bool usage_sort_args=false, SIZE_TYPE usage_width=78)

Set extra info to be used by PrintUsage().

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

Add description for optional key without default value.

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.

@ eDouble

Convertible into a floating point number (double)

@ eOutputFile

Name of file (must be writable)

@ eInteger

Convertible into an integer number (int or Int8)

#define ERR_POST(message)

Error posting with file, line number information but without error codes.

void Warning(CExceptionArgs_Base &args)

TObjectType * GetNonNullPointer(void)

Get pointer value and throw a null pointer exception if pointer is null.

void Reset(void)

Reset reference object.

bool NotEmpty(void) const THROWS_NONE

Check if CRef is not empty – pointing to an object and has a non-null value.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

static string IntToString(int value, TNumToStringFlags flags=0, int base=10)

Convert int to string.

static string kMaxValue("MaxValue")

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