// -*- mode: c++; indent-tabs-mode: nil; -*-
//
// Copyright 2009 Illumina, Inc.
//
// This software is covered by the "Illumina Genome Analyzer Software
// License Agreement" and the "Illumina Source Code License Agreement",
// and certain third party copyright/licenses, and any user of this
// source file is bound by the terms therein (see accompanying files
// Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
// Illumina_Source_Code_License_Agreement.pdf and third party
// copyright/license notices).
//
//

/// \file
///
/// \author Chris Saunders
///

#include "starling/align_path_bam_util.hh"

#include <cassert>


using namespace ALIGNPATH;



void
bam_cigar_to_apath(const uint32_t* bam_cigar,
                   const unsigned n_cigar,
                   path_t& apath){


    assert(n_cigar>0);
    apath.resize(n_cigar);
    for(unsigned i(0);i<n_cigar;++i){
        apath[i].length=(bam_cigar[i]>>BAM_CIGAR_SHIFT);
        apath[i].type = static_cast<align_t>(1+(bam_cigar[i]&BAM_CIGAR_MASK));
    }
}



void
apath_to_bam_cigar(const path_t& apath,
                   uint32_t* bam_cigar){

    const unsigned as(apath.size());
    for(unsigned i(0);i<as;++i){
        const path_segment& ps(apath[i]);
        assert(ps.type != NONE);
        bam_cigar[i] = (ps.length<<BAM_CIGAR_SHIFT | (static_cast<uint32_t>(ps.type)-1));
    }
}



void
edit_bam_cigar(const path_t& apath,
               bam1_t& br){

    bam1_core_t& bc(br.core);

    const int old_n_cigar(bc.n_cigar);
    const int new_n_cigar(apath.size());
    const int delta(4*(new_n_cigar-old_n_cigar));

    if(0 != delta) {
        const int end(bc.l_qname+(4*old_n_cigar));
        change_bam_data_segment_len(end,delta,br);
        bc.n_cigar=new_n_cigar;
    }

    //update content of cigar array:
    apath_to_bam_cigar(apath,bam1_cigar(&br));
}