// -*- 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 "indel.hh"

#include <iostream>



std::ostream&
operator<<(std::ostream& os, 
           const indel_key& ik){
    os << "INDEL pos: " << ik.pos << " type: " << INDEL::get_index_label(ik.type) << " len: " << ik.length << "\n";
    return os;
}



static
void
report_indel_evidence_set(const indel_data::evidence_t& e,
                          const char* label,
                          std::ostream& os) {
    typedef indel_data::evidence_t::const_iterator viter;
    viter i(e.begin()),i_end(e.end());
    for(unsigned n(0);i!=i_end;++i){
        os << label << " no: " << ++n << " id: " << *i << "\n";
    }
}



std::ostream&
operator<<(std::ostream& os,
           const read_path_scores& rps) {

    os << "ref: " << rps.ref
       << " indel: " << rps.indel
       << " nonsite: " << rps.nonsite;

    typedef read_path_scores::alt_indel_t::const_iterator aiter;
    aiter i(rps.alt_indel.begin()), i_end(rps.alt_indel.end());
    for(;i!=i_end;++i){
        const indel_key& ik(i->first);
        os << " alt-" << ik.pos << "-" << INDEL::get_index_label(ik.type) << ik.length << ": " << i->second;
    }

    return os;
}



std::ostream&
operator<<(std::ostream& os,
           const indel_data& id) {
    os << "seq: " << id.seq << "\n";

    report_indel_evidence_set(id.all_read_ids,"all_read",os);
    report_indel_evidence_set(id.contig_ids,"contig",os);
    report_indel_evidence_set(id.map_read_ids,"map_read",os);
    report_indel_evidence_set(id.submap_read_ids,"submap_read",os);

    {
        typedef indel_data::score_t::const_iterator siter;
        siter i(id.read_path_lnp.begin()), i_end(id.read_path_lnp.end());
        for(unsigned n(0);i!=i_end;++i){
            os << "read_path_lnp no: " << ++n
               << " id: " << i->first 
               << " " << i->second
               << "\n";
        }
    }

    report_indel_evidence_set(id.suboverlap_read_ids,"suboverlap_read",os);

    //os << "is_conflict? " << id.is_conflict << "\n";

    return os;
}



std::ostream&
operator<<(std::ostream& os,
           const indel& in) {

    os << in.key << in.data;

    return os;
}