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USING_SCOPE (objects) static CNcbiOstream & PrintTabularUnaligned (CNcbiOstream &ostr, const CMagicBlastResults &results, const TQueryMap &queries, bool first_seg, const string &user_tag) static CNcbiOstream & PrintSAMUnaligned (CNcbiOstream &ostr, const CMagicBlastResults &results, const TQueryMap &queries, bool first_seg, bool trim_read_ids, const string &user_tag) static char s_Complement (char c) static string s_GetBareId (const CSeq_id &id) static string s_GetSequenceId (const CBioseq &bioseq) static string s_GetFastaDefline (const CBioseq &bioseq) static void s_CreateQueryMap (const CBioseq_set &query_batch, TQueryMap &query_map) static const CBioseq & s_GetQueryBioseq (const TQueryMap &queries, const CSeq_id &seqid) static int s_GetQuerySequence (const CBioseq &bioseq, const CRange< TSeqPos > &range, bool reverse_complement, string &sequence) static bool s_GetQualityString (const CBioseq &bioseq, string &quality_str) static CNcbiOstream & PrintFastaUnaligned (CNcbiOstream &ostr, const CMagicBlastResults &results, const TQueryMap &queries, bool first_seg) static CNcbiOstream & PrintUnaligned (CNcbiOstream &ostr, CFormattingArgs::EOutputFormat fmt, const CMagicBlastResults &results, const TQueryMap &queries, bool first_seg, bool trim_read_ids, const string &user_tag) CNcbiOstream & PrintTabularHeader (CNcbiOstream &ostr, const string &version, const string &cmd_line_args, bool user_tag) 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 & PrintTabular (CNcbiOstream &ostr, CNcbiOstream &unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_fmt, const CMagicBlastResults &results, const TQueryMap &queries, bool is_paired, int batch_number, int &compartment, bool trim_read_id, bool print_unaligned, bool no_discordant, const string &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 & PrintSAMHeader (CNcbiOstream &ostr, CRef< CLocalDbAdapter > db_adapter, const string &cmd_line_args) static ENa_strand s_GetSpliceSiteOrientation (const CSpliced_seg::TExons::const_iterator &exon, const CSpliced_seg::TExons::const_iterator &next_exon) 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) static CNcbiOstream & PrintSAM (CNcbiOstream &ostr, CNcbiOstream &unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_fmt, CMagicBlastResults &results, const TQueryMap &queries, 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 & PrintSAM (CNcbiOstream &ostr, CNcbiOstream &unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_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 & PrintASN1 (CNcbiOstream &ostr, const CBioseq_set &query_batch, CSeq_align_set &aligns) ◆ SAM_FLAG_FIRST_SEGMENT ◆ SAM_FLAG_LAST_SEGMENT ◆ SAM_FLAG_MULTI_SEGMENTS ◆ SAM_FLAG_NEXT_REVCOMP ◆ SAM_FLAG_NEXT_SEG_UNMAPPED ◆ SAM_FLAG_SECONDARY ◆ SAM_FLAG_SEG_UNMAPPED ◆ SAM_FLAG_SEGS_ALIGNED ◆ SAM_FLAG_SEQ_REVCOMP ◆ TQueryMap ◆ TSeq_idHashSet ◆ 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().
◆ PrintFastaUnaligned() ◆ PrintSAM() [1/3] static CNcbiOstream& PrintSAM ( CNcbiOstream & ostr, CNcbiOstream & unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_fmt, CMagicBlastResults & results, const TQueryMap & queries, 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 ) static ◆ PrintSAM() [2/3] CNcbiOstream& PrintSAM ( CNcbiOstream & ostr, CNcbiOstream & unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_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 ) ◆ PrintSAM() [3/3] 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 ) static
Definition at line 1008 of file magicblast_util.cpp.
References _ASSERT, abs, context, BlastQueryInfo::contexts, CSeq_align_Base::C_Segs::e_Denseg, CSpliced_exon_chunk_Base::e_Genomic_ins, CSpliced_exon_chunk_Base::e_Match, CSpliced_exon_chunk_Base::e_Mismatch, CSpliced_exon_chunk_Base::e_Product_ins, CSeq_align_Base::C_Segs::e_Spliced, eFwdRev, eNa_strand_minus, eNa_strand_plus, NStr::EndsWith(), eNonSpecific, eRevFwd, CSeq_align::eScore_Score, fFirstSegmentFlag, CSeq_align::FindExt(), first(), fLastSegmentFlag, fPartialFlag, CSeq_align_set_Base::Get(), CUser_object_Base::GetData(), CSeq_align_Base::C_Segs::GetDenseg(), CSeq_align_Base::C_Segs::GetDisc(), CSpliced_seg_Base::GetExons(), CRange_Base::GetFrom(), CDense_seg_Base::GetLens(), CSeq_align::GetNamedScore(), CSpliced_seg_Base::GetProduct_length(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStrand(), CSeq_align_Base::C_Segs::GetSpliced(), CDense_seg_Base::GetStarts(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), i, int, NStr::IntToString(), CSeq_align_Base::C_Segs::IsDisc(), ITERATE, log10(), MAGICBLAST_MAX_INSERT_SIZE_NONSPLICED, MAGICBLAST_MAX_INSERT_SIZE_SPLICED, CSeq_id::Match(), MIN, NCBI_THROW, CConstRef< C, Locker >::NotEmpty(), r(), s_GetBareId(), s_GetQualityString(), s_GetQueryBioseq(), s_GetQuerySequence(), s_GetSequenceId(), s_GetSpliceSiteOrientation(), SAM_FLAG_FIRST_SEGMENT, SAM_FLAG_LAST_SEGMENT, SAM_FLAG_MULTI_SEGMENTS, SAM_FLAG_NEXT_REVCOMP, SAM_FLAG_NEXT_SEG_UNMAPPED, SAM_FLAG_SECONDARY, SAM_FLAG_SEGS_ALIGNED, SAM_FLAG_SEQ_REVCOMP, BlastContextInfo::segment_flags, NStr::Split(), NStr::StringToInt(), and CSeq_align_Base::C_Segs::Which().
Referenced by CMagicBlastThread::Main(), and PrintSAM().
◆ 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().
◆ PrintSAMUnaligned()Definition at line 1507 of file magicblast_util.cpp.
References NStr::EndsWith(), CMagicBlastResults::fFiltered, flags, info, results, s_GetQualityString(), s_GetQueryBioseq(), s_GetQuerySequence(), s_GetSequenceId(), SAM_FLAG_FIRST_SEGMENT, SAM_FLAG_LAST_SEGMENT, SAM_FLAG_MULTI_SEGMENTS, SAM_FLAG_NEXT_SEG_UNMAPPED, SAM_FLAG_SEG_UNMAPPED, and CSeq_id::Set().
Referenced by PrintUnaligned().
◆ PrintTabular() [1/3] static CNcbiOstream& PrintTabular ( CNcbiOstream & ostr, CNcbiOstream & unaligned_ostr, CFormattingArgs::EOutputFormat unaligned_fmt, const CMagicBlastResults & results, const TQueryMap & queries, bool is_paired, int batch_number, int & compartment, bool trim_read_id, bool print_unaligned, bool no_discordant, const string & user_tag ) static ◆ PrintTabular() [2/3] 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 ) ◆ PrintTabular() [3/3]Definition at line 441 of file magicblast_util.cpp.
References _ASSERT, eNa_strand_minus, CSeq_align::eScore_PercentIdentity_Gapped, CSeq_align::eScore_Score, CSeq_align::FindExt(), first(), CSeq_align_set_Base::Get(), CUser_object_Base::GetData(), CSeq_align_Base::C_Segs::GetDisc(), CRange_Base::GetFrom(), CBioseq_Base::GetInst(), CSeq_inst_Base::GetLength(), CSeq_align::GetNamedScore(), CSpliced_seg_Base::GetProduct_length(), CSeq_align_Base::GetSegs(), CSeq_align::GetSeq_id(), CSeq_align::GetSeqRange(), CSeq_align::GetSeqStart(), CSeq_align::GetSeqStrand(), CSeq_align_Base::C_Segs::GetSpliced(), CRange_Base::GetTo(), COpenRange< Position >::GetToOpen(), i, isalpha(), CSeq_align_Base::C_Segs::IsDenseg(), isdigit(), CSeq_align_Base::C_Segs::IsDisc(), CSpliced_seg_Base::IsSetProduct_length(), CSeq_align_Base::C_Segs::IsSpliced(), ITERATE, CSeq_id::Match(), MAX, MIN, CConstRef< C, Locker >::NotEmpty(), r(), s_Complement(), s_GetBareId(), s_GetQueryBioseq(), s_GetQuerySequence(), and s_GetSequenceId().
Referenced by CMagicBlastThread::Main(), and PrintTabular().
◆ PrintTabularHeader() ◆ PrintTabularUnaligned() ◆ PrintUnaligned() ◆ s_Complement() static char s_Complement ( char c ) static ◆ s_CreateQueryMap() ◆ s_GetBareId()Definition at line 156 of file magicblast_util.cpp.
References CObject_id_Base::GetId(), CObject_id_Base::GetStr(), CDbtag_Base::GetTag(), NStr::IntToString(), CObject_id_Base::IsId(), and CObject_id_Base::IsStr().
Referenced by PrintSAM(), PrintSAMHeader(), PrintTabular(), s_GetFastaDefline(), s_GetQueryBioseq(), and s_GetSequenceId().
◆ s_GetFastaDefline() ◆ s_GetQualityString() ◆ s_GetQueryBioseq() ◆ s_GetQuerySequence()Definition at line 250 of file magicblast_util.cpp.
References CSeqConvert::Convert(), CSeq_data_Base::e_Iupacna, CSeqUtil::e_Iupacna, CSeq_data_Base::e_Ncbi2na, CSeqUtil::e_Ncbi2na, CSeq_data_Base::e_Ncbi4na, CSeqUtil::e_Ncbi4na, CSeq_data_Base::e_Ncbi8na, CSeqUtil::e_Ncbi8na, CAliasBase< TPrim >::Get(), CRange_Base::GetFrom(), CBioseq_Base::GetInst(), CSeq_data_Base::GetIupacna(), COpenRange< Position >::GetLength(), CSeq_data_Base::GetNcbi2na(), CSeq_data_Base::GetNcbi4na(), CSeq_data_Base::GetNcbi8na(), CSeq_inst_Base::GetSeq_data(), COpenRange< Position >::IsWhole(), NCBI_THROW, COpenRange< Position >::NotEmpty(), reverse_complement(), CSeqManip::ReverseComplement(), tmp, and CSeq_data_Base::Which().
Referenced by PrintFastaUnaligned(), PrintSAM(), PrintSAMUnaligned(), and PrintTabular().
◆ s_GetSequenceId() ◆ s_GetSpliceSiteOrientation() static ENa_strand s_GetSpliceSiteOrientation ( const CSpliced_seg::TExons::const_iterator & exon, const CSpliced_seg::TExons::const_iterator & next_exon ) static ◆ USING_SCOPE()RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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