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

m_QueryOptions(query_opts),

m_DatabaseArgs(db_args),

m_FormattingArgs(fmt_args),

m_OutUnalignedStream(unaligned_stream)

kTrimReadIdForSAM =

(fr ==

|| rf ==

);

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

);

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

isDone =

;

(!kDbName.empty()) {

thread_db_adapter.

(

ostringstream the_unaligned_ostr;

ostringstream& unaligned_ostr =

*

->GetFlatResults(kNoDiscordant));

unaligned_ostr.str(

);

query_batch.

();

CRef< CSearchDatabase > GetSearchDatabase() const

Retrieve the search database information.

CRef< IQueryFactory > GetSubjects(objects::CScope *scope=NULL)

Retrieve subject sequences, if provided.

string GetDatabaseName() const

Get the BLAST database name.

void GetNextSeqBatch(CBioseq_set &bioseq_set)

EOutputFormat GetFormattedOutputChoice() const

Get the choice of formatted output.

@ eTabular

Tabular output.

@ eAsnText

ASN.1 text output.

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

CNcbiOstream * m_OutUnalignedStream

CRef< CBlastDatabaseArgs > m_DatabaseArgs

CNcbiOstream & m_OutStream

CRef< CMapperFormattingArgs > m_FormattingArgs

CMagicBlastThread(CBlastInputOMF &input, CRef< CMagicBlastOptionsHandle > options, CRef< CMapperQueryOptionsArgs > query_opts, CRef< CBlastDatabaseArgs > db_args, CRef< CMapperFormattingArgs > fmt_args, CNcbiOstream &out, CNcbiOstream *unaligned_stream)

CRef< CMapperQueryOptionsArgs > m_QueryOptions

virtual void * Main(void)

Derived (user-created) class must provide a real thread function.

CRef< CMagicBlastOptionsHandle > m_Options

bool TrimReadIds(void) const

Should read ids be in SAM format be trimmed of .1 and .2 endings for paired mapping.

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.

bool PrintMdTag(void) const

Should MD tag be included in SAM report.

bool NoDiscordant(void) const

Should non-concordant pairs be filtered out of report.

bool PrintUnaligned(void) const

Should unaligned reads be reported.

bool IsPaired(void) const

Are query sequences paired.

NCBI C++ Object Manager free implementation of IQueryFactory.

void SetNumberOfThreads(int num_threads, bool force_mt=false)

Setting the number of threads.

std::ofstream out("events_result.xml")

main entry point for tests

void SetNegativeGiList(CSeqDBGiList *gilist)

Mutator for the negative gi list.

bool GetPaired() const

Are the mapping reads assumed paired.

CRef< CMagicBlastResultSet > RunEx(void)

const CRef< CSeqDBGiList > & GetNegativeGiList() const

Accessor for the negative gi list.

CRef< CSeqDB > GetSeqDb() const

Obtain a reference to the database.

CRef< ILocalQueryData > MakeLocalQueryData(const CBlastOptions *opts)

Creates and caches an ILocalQueryData.

virtual BlastQueryInfo * GetQueryInfo()=0

Accessor for the BlastQueryInfo structure.

const CBlastOptions & GetOptions() const

Return the object which this object is a handle for.

const CRef< CSeqDBGiList > & GetGiList() const

Accessor for the gi list.

bool GetSpliceAlignments() const

Return the splice/unsplice alignments switch value.

void SetGiList(CSeqDBGiList *gilist)

Mutator for the gi list.

@ eBlastDbIsNucleotide

nucleotide

#define NCBI_THROW(exception_class, err_code, message)

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

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.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

bool IsSetSeq_set(void) const

Check if a value has been assigned to Seq_set data member.

const TSeq_set & GetSeq_set(void) const

Get the Seq_set member data.

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

CNcbiOstream & PrintASN1(CNcbiOstream &ostr, const CBioseq_set &query_batch, CSeq_align_set &aligns)

static CNcbiOstream & PrintTabular(CNcbiOstream &ostr, const CSeq_align &align, const TQueryMap &queries, bool is_paired, int batch_number, int compartment, const string &user_tag, const CSeq_align *mate=NULL)

static CNcbiOstream & PrintSAM(CNcbiOstream &ostr, const CSeq_align &align, const TQueryMap &queries, const BlastQueryInfo *query_info, bool is_spliced, int batch_number, bool &first_secondary, bool &last_secondary, bool trim_read_ids, E_StrandSpecificity strand_specific, bool only_specific, bool print_md_tag, bool other=false, const string &user_tag="", const CSeq_align *mate=NULL)

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

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