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NCBI C++ ToolKit: src/app/magicblast/magicblast_util.hpp Source File

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32 #ifndef APP_MAGICBLAST___MAGICBLAST_UTILS__HPP 33 #define APP_MAGICBLAST___MAGICBLAST_UTILS__HPP 50  const string

& cmd_line_args);

66  const string

& user_tag);

69  const string

& cmd_line_args,

bool

user_tag);

76  bool

is_paired,

int

batch_number,

80  const string

& user_tag);

Interface for converting blast-related command line arguments into blast options.

EOutputFormat

Defines the output formats supported by our command line formatter.

Results of Magic-BLAST mapping.

#define END_NCBI_SCOPE

End previously defined NCBI scope.

#define END_SCOPE(ns)

End the previously defined scope.

#define BEGIN_NCBI_SCOPE

Define ncbi namespace.

#define BEGIN_SCOPE(ns)

Define a new scope.

IO_PREFIX::ostream CNcbiOstream

Portable alias for ostream.

Declares class which provides internal BLAST database representations to the internal BLAST APIs.

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

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)

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

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

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)

const string version

version string

The query related information.

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