// -*- 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 "blt_util/bam_dumper.hh"
#include "starling/starling_streams.hh"

#include <cassert>

#include <fstream>
#include <iostream>



starling_streams::
starling_streams(const starling_options& client_opt,
                 const prog_info& pinfo,
                 const char* const cmdline,
                 const bam_header_t* const header)
    : base_t(client_opt,pinfo,cmdline,true) {

    if(client_opt.is_bindel_diploid_file){
        std::ofstream* fosptr(new std::ofstream);
        _bindel_diploid_osptr.reset(fosptr);
        std::ofstream& fos(*fosptr);
        open_ofstream(pinfo,client_opt.bindel_diploid_filename,"bindel-diploid",client_opt.is_clobber,fos);

        fos << "# ** " << pinfo.name() << " bindel-diploid file **\n";
        write_file_audit(client_opt,pinfo,cmdline,fos);
        fos << "#$ INDEL_THETA " << client_opt.bindel_diploid_theta << "\n";
        fos << "#\n";
        fos << "#$ COLUMNS seq_name pos type ref_upstream ref/indel ref_downstream Q(indel) max_gtype Q(max_gtype) depth alt_reads indel_reads other_reads repeat_unit ref_repeat_count indel_repeat_count\n";
    }

    if(client_opt.is_realigned_read_file){
        assert(NULL != header);

        // \TODO consider putting extra info into BAM header:
        //
        //fp->header = bam_header_dup((const bam_header_t*)aux);
        //fos << "@PG\tID:" << pinfo.name() << "\tVN:" << pinfo.version() << "\tCL:" << cmdline << "\n";

        if(not client_opt.is_clobber){ // weak clobber test:
            std::ofstream fos;
            open_ofstream(pinfo,client_opt.realigned_read_filename,"realigned-read BAM",client_opt.is_clobber,fos);
        }    
        _realign_bam_ptr.reset(new bam_dumper(client_opt.realigned_read_filename.c_str(),header));
    }
}



// dtor here to make auto_ptr work correctly:
starling_streams::
~starling_streams() {}