sam.cpp

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/* $Id:
* ===========================================================================
*
*                            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 offical duties as a United States Government employee and
*  thus cannot be copyrighted.  This software/database is freely available
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*  may be obtained by using this software or data. The NLM and the U.S.
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*  warranties of performance, merchantability or fitness for any particular
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*  Please cite the author in any work or product based on this material.
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* Author: Amelia Fong
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/// @file: tabular.cpp
/// Formatting of pairwise sequence alignments in tabular form.
/// One line is printed for each alignment with tab-delimited fielalnVec.
 
#include <ncbi_pch.hpp>
 
#include <algo/blast/format/sam.hpp>
#include <serial/iterator.hpp>
#include <objtools/align_format/align_format_util.hpp>
 
BEGIN_NCBI_SCOPE
USING_SCOPE(objects);
 
CBlast_SAM_Formatter::CBlast_SAM_Formatter(CNcbiOstream& out, CScope& scope,
                                           const string & custom_spec,
                                           const CSAM_Formatter::SProgramInfo & info) :
                                           CSAM_Formatter(out,scope),
                                           m_refRow(1)
{
    CSAM_Formatter::SetFlag(CSAM_Formatter::fSAM_PlainSeqIds);
    x_ProcessCustomSpec(custom_spec, info);
}
 
void CBlast_SAM_Formatter::x_Print(const CSeq_align_set & aln)
{
    if(m_refRow == 1) {
        CSeq_align_set sorted;
        sorted.Set() = aln.Get();
        sorted.Set().sort(align_format::CAlignFormatUtil::SortHspByMasterStartAscending);
        CSAM_Formatter::Print(sorted, m_refRow);
    }
    else {
        CSAM_Formatter::Print(aln, m_refRow);
    }
}
 
void CBlast_SAM_Formatter::Print(const CSeq_align_set &  aln)
{
    if (aln.Get().front()->GetSegs().Which() == CSeq_align::C_Segs::e_Dendiag){
        CSeq_align_set d_aln;
        ITERATE(CSeq_align_set::Tdata, itr, aln.Get()){
            CRef<CSeq_align> dense_seg = align_format::CAlignFormatUtil::CreateDensegFromDendiag(**itr);
            CDense_seg::TScores & scores = dense_seg->SetSegs().SetDenseg().SetScores();
            dense_seg->SetScore().swap(scores);
            d_aln.Set().push_back(dense_seg);
        }
        x_Print(d_aln);
    }
    else {
        x_Print(aln);
    }
}
 
void CBlast_SAM_Formatter::x_ProcessCustomSpec(const string & custom_spec,
                                               const CSAM_Formatter::SProgramInfo & info)
{
    vector<string> format_tokens;
    NStr::Split(custom_spec, " ", format_tokens);
    CSAM_Formatter::SetProgram(info);
    m_refRow = 1;
    ITERATE (vector<string>, iter, format_tokens) {
         if("SR" == *iter) {
            m_refRow = 0;
         }
         if ("SQ" == *iter) {
            CSAM_Formatter::SetFlag(CSAM_Formatter::fSAM_SeqData);
        }
    }
 
    if(m_refRow == 1) {
        CSAM_Formatter::SetGroupOrder(eGO_Reference);
        CSAM_Formatter::SetSortOrder(eSO_Coordinate);
    }
}
 
 
END_NCBI_SCOPE