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CNcbiOstream & PrintSAMHeader (CNcbiOstream &ostr, CRef< CLocalDbAdapter > db_adapter, const string &cmd_line_args) CNcbiOstream & PrintSAM (CNcbiOstream &ostr, CNcbiOstream &unaligned_ostr, CFormattingArgs::EOutputFormat fmt, const CMagicBlastResultSet &results, const CBioseq_set &query_batch, const BlastQueryInfo *query_info, bool is_spliced, int batch_number, bool trim_read_id, bool print_unaligned, bool no_discordant, E_StrandSpecificity strand_specific, bool only_specific, bool print_md_tag, const string &user_tag) CNcbiOstream & PrintTabularHeader (CNcbiOstream &ostr, const string &version, const string &cmd_line_args, bool user_tag) CNcbiOstream & PrintTabular (CNcbiOstream &ostr, CNcbiOstream &unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_fmt, const CMagicBlastResultSet &results, const CBioseq_set &query_batch, bool is_paired, int batch_number, bool trim_read_id, bool print_unaligned, bool no_discordant, const string &user_tag) CNcbiOstream & PrintASN1 (CNcbiOstream &ostr, const CBioseq_set &query_batch, CSeq_align_set &aligns) ◆ E_StrandSpecificity ◆ PrintASN1()Definition at line 1696 of file magicblast_util.cpp.
References CSeq_id_Base::e_Local, CSeq_align_Base::C_Segs::e_Spliced, CSeq_descr_Base::Get(), CBioseq_Base::GetDescr(), CBioseq_Base::IsSetDescr(), MSerial_AsnText, CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), s_CreateQueryMap(), s_GetQueryBioseq(), CSeq_align_set_Base::Set(), and NStr::Split().
Referenced by CMagicBlastThread::Main().
◆ PrintSAM() CNcbiOstream& PrintSAM ( CNcbiOstream & ostr, CNcbiOstream & unaligned_ostr, CFormattingArgs::EOutputFormat fmt, const CMagicBlastResultSet & results, const CBioseq_set & query_batch, const BlastQueryInfo * query_info, bool is_spliced, int batch_number, bool trim_read_id, bool print_unaligned, bool no_discordant, E_StrandSpecificity strand_specific, bool only_specific, bool print_md_tag, const string & user_tag ) ◆ PrintSAMHeader()Definition at line 848 of file magicblast_util.cpp.
References _ASSERT, BLAST_SEQSRC_EOF, CSeq_id::BlastRank(), BlastSeqSrcIteratorFree(), BlastSeqSrcIteratorNew(), BlastSeqSrcIteratorNext(), BlastSeqSrcResetChunkIterator(), CLocalDbAdapter::GetSearchDatabase(), CSearchDatabase::GetSeqDb(), GetSequenceLengthAndId(), CSeqDB::GetTaxIDs(), CLocalDbAdapter::IsBlastDb(), CLocalDbAdapter::MakeSeqInfoSrc(), CLocalDbAdapter::MakeSeqSrc(), CRef< C, Locker >::NotEmpty(), CRef< C, Locker >::Reset(), and s_GetBareId().
Referenced by CMagicBlastApp::Run().
◆ PrintTabular() CNcbiOstream& PrintTabular ( CNcbiOstream & ostr, CNcbiOstream & unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_fmt, const CMagicBlastResultSet & results, const CBioseq_set & query_batch, bool is_paired, int batch_number, bool trim_read_id, bool print_unaligned, bool no_discordant, const string & user_tag ) ◆ PrintTabularHeader()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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