splign_exon_trim.hpp

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#ifndef ALGO_ALIGN_SPLIGN_EXON_TRIM_HPP
#define ALGO_ALIGN_SPLIGN_EXON_TRIM_HPP
 
/* $Id: splign_exon_trim.hpp 100425 2023-07-31 13:44:51Z mozese2 $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE                          
*               National Center for Biotechnology Information
*                                                                          
*  This software/database is a "United States Government Work" under the   
*  terms of the United States Copyright Act.  It was written as part of    
*  the author's official duties as a United States Government employee and 
*  thus cannot be copyrighted.  This software/database is freely available 
*  to the public for use. The National Library of Medicine and the U.S.    
*  Government have not placed any restriction on its use or reproduction.  
*                                                                          
*  Although all reasonable efforts have been taken to ensure the accuracy  
*  and reliability of the software and data, the NLM and the U.S.          
*  Government do not and cannot warrant the performance or results that    
*  may be obtained by using this software or data. The NLM and the U.S.    
*  Government disclaim all warranties, express or implied, including       
*  warranties of performance, merchantability or fitness for any particular
*  purpose.                                                                
*                                                                          
*  Please cite the author in any work or product based on this material.   
*
* ===========================================================================
*
* Author: Boris Kiyutin
*
* File Description: exon trimming (alignment post processing step)
*                   
* ===========================================================================
*/
 
 
#include <algo/align/nw/nw_formatter.hpp>
#include <algo/align/nw/nw_spliced_aligner.hpp>
#include <algo/align/splign/splign.hpp>
 
BEGIN_NCBI_SCOPE
 
 
//trimming of spliced alignments
class CSplignTrim {
public:
 
    typedef CNWFormatter::SSegment TSeg; //AKA CSplign::TSegment
    typedef vector<TSeg> TSegs;          //AKA CSplign::TSegments
 
    CSplignTrim(const char *seq, int seqlen, CConstRef<CSplicedAligner> aligner, double max_part_exon_drop) : m_seq(seq), m_seqlen(seqlen), m_aligner(aligner), m_MaxPartExonIdentDrop(max_part_exon_drop)
    {
    }
 
    //check if the exon segments[p] abuts another exon in genomic coordinates
    static bool HasAbuttingExonOnRight(TSegs segments, TSeqPos p);
    //same check on the left side
    static bool HasAbuttingExonOnLeft(TSegs segments, TSeqPos p);
 
    //legacy check
    //if two short throws away and reterns true
    //otherwise returns false   
    bool ThrowAwayShortExon(TSeg& s);
 
    bool ThrowAway20_28_90(TSeg& s);
 
    //cut len bases from left
    //len is length on alignment to cut
    void CutFromLeft(size_t len, TSeg& s);
 
    void CutToMatchLeft(TSeg& s);
    void Cut50FromLeft(TSeg& s);
    void ImproveFromLeft(TSeg& s);
 
    //cut len bases from right
    //len is length on alignment to cut
    void CutFromRight(size_t len, TSeg& s);
 
    void CutToMatchRight(TSeg& s);
    void Cut50FromRight(TSeg& s);
    void ImproveFromRight(TSeg& s);
 
    // aka stich holes
    //joins exons segments[p1] and segments[p1] into a singe exon
    //everithing in between becomes a regular gap in query adjacent to a regular gap in subject 
    void JoinExons(TSegs& segments, TSeqPos p1, TSeqPos p2);
 
    //trims exons around internal alignment gaps to complete codons
    //if CDS can be retrieved from bioseq
    void TrimHolesToCodons(TSegs& segments, objects::CBioseq_Handle& mrna_bio_handle, bool mrna_strand, TSeqPos mrna_len);
 
    // updates m_annot for a segment based on SSegment::m_box and CSplignTrim:m_seq
    void UpdateAnnot(TSeg& s);
 
    // implies s.exon, s.m_box, and s.m_details are correct
    // updates the rest of segment fields including m_annot
    void Update(TSeg& s);
 
    void AdjustGaps(TSegs& segments);
 
private:
    const char *m_seq;//genomic sequence
    const int m_seqlen;
    CConstRef<CSplicedAligner> m_aligner;
    const double m_MaxPartExonIdentDrop; 
};
 
END_NCBI_SCOPE
 
#endif