src/algo/align/contig_assembly/contig_assembly.cpp File Reference

#include <ncbi_pch.hpp>
#include <corelib/ncbi_system.hpp>
#include <algo/align/contig_assembly/contig_assembly.hpp>
#include <objects/seqloc/Seq_loc.hpp>
#include <objects/seqloc/Seq_id.hpp>
#include <objmgr/scope.hpp>
#include <algo/blast/api/blast_types.hpp>
#include <algo/blast/api/bl2seq.hpp>
#include <algo/blast/api/blast_options_handle.hpp>
#include <algo/blast/api/blast_nucl_options.hpp>
#include <objects/seqalign/Seq_align.hpp>
#include <objects/seqalign/Seq_align_set.hpp>
#include <objects/seqalign/Dense_seg.hpp>
#include <objmgr/seq_vector.hpp>
#include <objmgr/util/sequence.hpp>
#include <algo/align/nw/nw_band_aligner.hpp>
#include <algo/align/nw/align_exception.hpp>
#include <objtools/alnmgr/alnvec.hpp>
#include <algo/dustmask/symdust.hpp>

Include dependency graph for contig_assembly.cpp:

Go to the source code of this file.

Functions
	USING_SCOPE (objects)
	USING_SCOPE (blast)
static void	s_SplitCommandLine (string s, vector< string > &result)
static void	s_GetTails (const CAlnVec &vec, vector< CContigAssembly::SAlignStats::STails > &tails)

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Function Documentation

static void s_GetTails (  const CAlnVec &  vec, vector< CContigAssembly::SAlignStats::STails > &  tails )  [static]

Definition at line 109 of file contig_assembly.cpp. References CAlnVec::GetBioseqHandle(), CBioseq_Handle::GetBioseqLength(), CAlnMap::GetNumRows(), CAlnMap::GetSeqStart(), CAlnMap::GetSeqStop(), CAlnMap::IsPositiveStrand(), CContigAssembly::SAlignStats::STails::left, and CContigAssembly::SAlignStats::STails::right.

static void s_SplitCommandLine (  string  s, vector< string > &  result )  [static]

Definition at line 62 of file contig_assembly.cpp.

USING_SCOPE (  blast   )

USING_SCOPE (  objects   )

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