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USING_SCOPE (objects) CCompactSAMApplication::Exon GetNextExon (string &cigar_string, string &MD_tag, int qfrom, int sfrom) int ProcessSAM (const vector< string > &tags, vector< CCompactSAMApplication::Exon > &exons) void Print (const CCompactSAMApplication::AlignInfo &ai) string Tag (const string &name, int value) string Tag (const string &name, const string &value) template<typename T > void ReplaceTag (vector< string > &fields, const string &name, const T &value) void RemoveTag (vector< string > &fields, const string &name) void FormatPaired (CCompactSAMApplication::AlignInfo &ai, int mate, int strand, int count, int index, bool left) void FormatSingle (CCompactSAMApplication::AlignInfo &ai, int mate, int strand, int count, int index, bool all_aligned) int main (int argc, const char *argv[]) ◆ FormatPaired() ◆ FormatSingle() ◆ GetNextExon()Definition at line 99 of file compact_sam.cpp.
References exit(), isdigit(), len, CCompactSAMApplication::Exon::m_align_len, CCompactSAMApplication::Exon::m_indels, CCompactSAMApplication::Exon::m_matches, CCompactSAMApplication::Exon::m_mismatches, CCompactSAMApplication::Exon::m_qfrom, CCompactSAMApplication::Exon::m_qto, CCompactSAMApplication::Exon::m_sfrom, and CCompactSAMApplication::Exon::m_sto.
Referenced by ProcessSAM().
◆ main() ◆ Print()Definition at line 242 of file compact_sam.cpp.
References i, and CCompactSAMApplication::AlignInfo::m_fields.
Referenced by CSplignFormatter::AsSeqAlignSet(), BlastdbCopyApplication::BlastdbCopyApplication(), CBlastDBAliasApp::CBlastDBAliasApp(), CBlastDbCheckApplication::CBlastDbCheckApplication(), CBlastDBCmdApp::CBlastDBCmdApp(), CBlastdbConvertApp::CBlastdbConvertApp(), CBlastFormatterApp::CBlastFormatterApp(), CBlastFormatterVdbApp::CBlastFormatterVdbApp(), CBlastnApp::CBlastnApp(), CBlastpApp::CBlastpApp(), CBlastVdbCmdApp::CBlastVdbCmdApp(), CBlastxApp::CBlastxApp(), CConvert2BlastMaskApplication::CConvert2BlastMaskApplication(), CDeltaBlastApp::CDeltaBlastApp(), CMagicBlastApp::CMagicBlastApp(), CMakeBlastDBApp::CMakeBlastDBApp(), CMakeClusterDBApp::CMakeClusterDBApp(), CMakeProfileDBApp::CMakeProfileDBApp(), CNcbiApplogApp::Cmd_Health(), CMultiApplication::CMultiApplication(), CArgDescriptions::CPrintUsageXml::CPrintUsageXml(), CPsiBlastApp::CPsiBlastApp(), CRPSBlastApp::CRPSBlastApp(), CRPSTBlastnApp::CRPSTBlastnApp(), CTblastnApp::CTblastnApp(), CTblastxApp::CTblastxApp(), CVDBBlastnApp::CVDBBlastnApp(), CVDBTblastnApp::CVDBTblastnApp(), FormatPaired(), FormatSingle(), CBlastFormatterApp::Init(), CSeedTopApp::Init(), CBlastDBAliasApp::Init(), CBlastdbConvertApp::Init(), CBlastDBCmdApp::Init(), CMakeBlastDBApp::Init(), CMakeClusterDBApp::Init(), CBlastFormatterVdbApp::Init(), CIgBlastnApp::Init(), CIgBlastpApp::Init(), CVecScreenApp::Init(), CCgiApplication::LogRequest(), SInteractiveNewRequestStart::SExtra::Print(), CBiosampleFieldDiff::Print(), CMagicBlastApp::Run(), CProjBulderApp::Run(), CProgramDescriptionArgs::SetArgumentDescriptions(), CQueue::x_DumpJobs(), CBlastFormat::x_InitSAMFormatter(), CNcbiApplicationAPI::x_LogOptions(), and CMakeProfileDBApp::x_SetupArgDescriptions().
◆ ProcessSAM() ◆ RemoveTag() ◆ ReplaceTag() ◆ Tag() [1/2] ◆ Tag() [2/2] ◆ USING_SCOPE() ◆ USING_NCBI_SCOPERetroSearch is an open source project built by @garambo | Open a GitHub Issue
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