#include <ncbi_pch.hpp>
#include <corelib/ncbiexpt.hpp>
#include <corelib/ncbi_system.hpp>
#include <math.h>
#include <algo/align/ngalign/merge_aligner.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 <algo/blast/api/disc_nucl_options.hpp>
#include <algo/align/util/score_builder.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 <algo/blast/api/local_blast.hpp>
#include <algo/blast/blastinput/blastn_args.hpp>
#include <algo/sequence/align_cleanup.hpp>
#include <algo/align/util/genomic_compart.hpp>

Include dependency graph for merge_aligner.cpp:

Go to the SVN repository for this file.

Functions
	USING_SCOPE (objects)

static bool	s_SortByAlignedLength (const CRef< objects::CSeq_align > &A, const CRef< objects::CSeq_align > &B)

static bool	s_SortByScore (const CRef< objects::CSeq_align > &A, const CRef< objects::CSeq_align > &B)