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NCBI C++ ToolKit: src/app/magicblast/magicblast_app.cpp Source File

num_db_sequences);

);

ss <<

<<

<<

<< ends;

& subject_length,

db_adapter.

();

(scope.

()) {

( (subjects = db_args->GetSubjects(scope)) ) {

IOS_BASE::iostate orig_state =

.rdstate();

IOS_BASE::fmtflags orig_flags =

.setf(ios::skipws);

.flags(orig_flags);

.setstate(orig_state);

(

=0;

<

.Size();

++) {

+=

[

] +

;

kSamLargeNumSubjects =

;

.Set(

,

);

num_db_sequences;

(fr ==

|| rf ==

);

(!only_specific && (fr || rf)) {

);

(only_specific && !(fr || rf)) {

(num_db_sequences < kSamLargeNumSubjects) {

batch_num = 500000;

num_seqs_str =

.Get(

);

(!num_seqs_str.empty()) {

batch_size =

(batch_size / num_threads, 5000000);

.SetMaxBatchNumSeqs(batch_num);

(

=0;

< num_threads;

++) {

threads[

]->

();

(

=0;

< num_threads;

++) {

threads[

]->

();

(

)db_size, (

)num_db_sequences);

num_db_sequences)

(

->GetNumGis()) {

(

->GetNumSis()){

(

->GetNumTaxIds()){

(

->GetNumPigs()) {

(

->GetNumGis()) {

(

->GetNumSis()){

(

->GetNumTaxIds()){

(

->GetNumPigs()) {

vector<CAlignFormatUtil::SDbInfo> dbinfo;

Produce formatted blast output for command line applications.

#define CATCH_ALL(exit_code)

Standard catch statement for all BLAST command line programs.

#define BLAST_EXIT_SUCCESS

Command line binary exit code: success.

Interface for reading SRA sequences into blast input.

Int4 BlastSeqSrcGetNumSeqs(const BlastSeqSrc *seq_src)

Get the number of sequences contained in the sequence source.

Int8 BlastSeqSrcGetTotLen(const BlastSeqSrc *seq_src)

Get the total length of all sequences in the sequence source.

Class representing a text or binary file containing sequences in ASN.1 format as a collection of Seq-...

static void GetBlastDbInfo(vector< SDbInfo > &retval, const string &blastdb_names, bool is_protein, int dbfilt_algorithm, bool is_remote=false)

Retrieve BLAST database information for presentation in BLAST report.

virtual CNcbiIstream & GetInputStream()

Get the input stream.

size_t GetNumThreads() const

Get the number of threads to spawn.

CRef< CBlastOptionsHandle > SetOptions(const CArgs &args)

Extract the command line arguments into a CBlastOptionsHandle object.

CRef< CBlastDatabaseArgs > GetBlastDatabaseArgs() const

Get the BLAST database arguments.

CArgDescriptions * SetCommandLine()

Set the command line arguments.

CRef< CQueryOptionsArgs > GetQueryOptionsArgs() const

Get the options for the query sequence(s)

CRef< CFormattingArgs > GetFormattingArgs() const

Get the formatting options.

bool ProduceDebugOutput() const

Return whether debug (verbose) output should be produced on remote searches (only available when comp...

virtual CNcbiOstream & GetOutputStream()

Get the output stream.

Encapsulates ALL the BLAST algorithm's options.

void AddParam(EUsageParams p, int val)

void DebugDumpText(ostream &out, const string &bundle, unsigned int depth) const

EOutputFormat GetFormattedOutputChoice() const

Get the choice of formatted output.

@ eTabular

Tabular output.

Defines user input exceptions.

Interface to create a BlastSeqSrc suitable for use in CORE BLAST from a a variety of BLAST database/s...

Handles command line arguments for blastmapper binary.

bool HasUnalignedOutputStream(void) const

Has a separate output stream for unaligned reads been set up.

virtual int GetQueryBatchSize() const

@inheritDoc

CNcbiOstream * GetUnalignedOutputStream(void) const

Get output stream for unaligned reads or NULL if it was not set up.

virtual void Init()

@inheritDoc

CBlastUsageReport m_UsageReport

void x_LogBlastSearchInfo(CBlastUsageReport &report, const CBlastOptions &options, CRef< CMapperFormattingArgs > fmt_args, CRef< CLocalDbAdapter > db_adapter, Int8 db_size, Int8 num_db_sequences)

CRef< CMagicBlastAppArgs > m_CmdLineArgs

This application's command line args.

CMagicBlastApp()

@inheritDoc

virtual int Run()

@inheritDoc

Handle to the nucleotide mapping options to the BLAST algorithm.

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

const string & GetUserTag(void) const

Get a user tag added to each alignment.

bool SelectFwdRev(void) const

Specify fwd/ref strands.

EOutputFormat GetUnalignedOutputFormat(void) const

Get format choice for unaligned reads.

bool SelectRevFwd(void) const

Specify rev/fwd strands.

bool SelectOnlyStrandSpecific(void) const

Specify only-strand-specific.

Argument class to collect query options for BLAST Mapper.

bool IsSraCacheEnabled(void) const

Is SRA caching in local files enabled (see File Caching at https://github.com/ncbi/sra-tools/wiki/Too...

const vector< string > & GetSraAccessions(void) const

Get a list of SRA accessions.

bool HasMateInputStream(void) const

Does the mate input stream exits.

EInputFormat GetInputFormat(void) const

Are queries provided in Fastc format.

bool IsPaired(void) const

Are query sequences paired.

EInputFormat

Input formats.

CNcbiIstream * GetMateInputStream(void) const

Get input stream for query mates.

Uint8 GetTotalLength() const

Returns the sum of the lengths of all available sequences.

int GetNumSeqs() const

Returns the number of sequences available.

EInputFormat

Input formats.

@ eNotFoundDb

DB main file not found.

virtual TErrCode GetErrCode(void) const

Class for reading sequences from SRA respository or SRA file.

void Print(const CCompactSAMApplication::AlignInfo &ai)

static const char * str(char *buf, int n)

string GetDatabaseName() const

Accessor for the database name.

const CRef< CSeqDBGiList > & GetNegativeGiList() const

Accessor for the negative gi list.

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

bool IsBlastDb() const

Returns true if this object represents a BLAST database.

bool GetLookupDbFilter(void) const

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

CRef< CBlastOptions > Clone() const

Explicit deep copy of the Blast options object.

const CRef< CSeqDBGiList > & GetGiList() const

Accessor for the gi list.

CRef< CSearchDatabase > GetSearchDatabase()

void SetFullVersion(CRef< CVersionAPI > version)

Set version data for the program.

void HideStdArgs(THideStdArgs hide_mask)

Set the hide mask for the Hide Std Flags.

virtual const CArgs & GetArgs(void) const

Get parsed command line arguments.

int AppMain(int argc, const char *const *argv, const char *const *envp=0, EAppDiagStream diag=eDS_Default, const char *conf=NcbiEmptyCStr, const string &name=NcbiEmptyString)

Main function (entry point) for the NCBI application.

CVersionInfo GetVersion(void) const

Get the program version information.

virtual void SetupArgDescriptions(CArgDescriptions *arg_desc)

Setup the command line argument descriptions.

const CNcbiArguments & GetArguments(void) const

Get the application's cached unprocessed command-line arguments.

@ fHideXmlHelp

Hide XML help description.

@ fHideLogfile

Hide log file description.

@ fHideFullVersion

Hide full version description.

@ fHideDryRun

Hide dryrun description.

@ fHideConffile

Hide configuration file description.

void SetDiagPostPrefix(const char *prefix)

Specify a string to prefix all subsequent error postings with.

EDiagSev SetDiagPostLevel(EDiagSev post_sev=eDiag_Error)

Set the threshold severity for posting the messages.

@ eDiag_Warning

Warning message.

#define NCBI_THROW(exception_class, err_code, message)

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

static void SplitPath(const string &path, string *dir=0, string *base=0, string *ext=0)

Split a path string into its basic components.

static CRef< CObjectManager > GetInstance(void)

Return the existing object manager or create one.

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.

bool Empty(void) const THROWS_NONE

Check if CRef is empty – not pointing to any object, which means having a null value.

int64_t Int8

8-byte (64-bit) signed integer

uint64_t Uint8

8-byte (64-bit) unsigned integer

bool IsEnabled(void)

Indicates whether application usage statistics collection is enabled for a current reporter instance.

IO_PREFIX::istream CNcbiIstream

Portable alias for istream.

IO_PREFIX::streampos CNcbiStreampos

Portable alias for streampos.

static int StringToInt(const CTempString str, TStringToNumFlags flags=0, int base=10)

Convert string to int.

bool Run(TRunMode flags=fRunDefault)

Run the thread.

void Join(void **exit_data=0)

Wait for the thread termination.

double Elapsed(void) const

Return time elapsed since first Start() or last Restart() call (in seconds).

void Start(void)

Start the timer.

Declares CMagicBlast, the C++ API for the BLAST RNA-Seq mapping engine.

static CBlastInputSourceOMF * s_CreateInputSource(CRef< CMapperQueryOptionsArgs > query_opts, CRef< CMagicBlastAppArgs > cmd_line_args)

static const int kMinorVersion

static const int kMajorVersion

int NcbiSys_main(int argc, ncbi::TXChar *argv[])

static CShortReadFastaInputSource::EInputFormat s_QueryOptsInFmtToFastaInFmt(CMapperQueryOptionsArgs::EInputFormat infmt)

static void s_InitializeSubject(CRef< blast::CBlastDatabaseArgs > db_args, CRef< blast::CBlastOptionsHandle > opts_hndl, CRef< blast::CLocalDbAdapter > &db_adapter, Uint8 &subject_length, int &num_sequences)

static string s_GetCmdlineArgs(const CNcbiArguments &a)

static const int kPatchVersion

static bool s_IsIStreamEmpty(CNcbiIstream &in)

CNcbiOstream & PrintSAMHeader(CNcbiOstream &ostr, CRef< CLocalDbAdapter > db_adapter, const string &cmd_line_args)

CNcbiOstream & PrintTabularHeader(CNcbiOstream &ostr, const string &version, const string &cmd_line_args, bool user_tag)

const string version

version string

#define INT4_MAX

largest nubmer represented by signed int

#define MAX(a, b)

returns larger of a and b.

Defines the CNcbiApplication and CAppException classes for creating NCBI applications.

std::istream & in(std::istream &in_, double &x_)

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

NOTE: This file contains work in progress and the APIs are likely to change, please do not rely on th...

static SLJIT_INLINE sljit_ins l(sljit_gpr r, sljit_s32 d, sljit_gpr x, sljit_gpr b)

Complete type definition of Blast Sequence Source ADT.

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