// -*- 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
///

#ifndef __STARLING_READ_SEGMENT_HH
#define __STARLING_READ_SEGMENT_HH


#include "alignment.hh"
#include "starling_read_key.hh"

#include <iosfwd>
#include <map>


typedef std::map<align_id_t,alignment> contig_align_t;
typedef uint8_t seg_id_t;
struct starling_read;


// class spun-off from starling read to represent the notion of exons
// without forcing a re-rig the entire starling design: as of now
// read-segment captures the concept of a read (sub-)segment for the
// purposes of realignment/pileup, etc. while starling_read aggregates
// all information associated with the full cluster.
//
struct read_segment {

    read_segment(const uint16_t size=0,
                 const uint16_t offset=0,
                 const starling_read* sread_ptr=NULL)
        : realign_path_lnp(0),
          is_realigned(false),
          _size(size),
          _offset(offset),
          _sread_ptr(sread_ptr) {}

    bool
    is_treated_as_usable_mapping() const;

    unsigned read_size() const { return _size; }
    bam_seq get_bam_read() const;
    const uint8_t* qual() const;

    const contig_align_t&
    contig_align() const;

    // are there any alignments without indels above max_indel_size?
    bool
    is_any_nonovermax(const unsigned max_indel_size) const;

    // check that information is valid and self-consistent;
    bool is_valid() const;

    const alignment&
    genome_align() const { return _genome_align; }

    // these methods just repeat from the parent read:
    align_id_t
    id() const;

    read_key
    key() const;

    bool
    is_genome_align_usable_mapping() const;

    uint8_t
    map_qual() const;

    std::pair<bool,bool>
    get_segment_edge_pin() const;

private:
    friend struct starling_read;

    bool
    is_full_segment() const;

    const starling_read& sread() const { return *_sread_ptr; }

private:
    alignment _genome_align;
public:
    alignment realignment;
    float realign_path_lnp;
    bool is_realigned;

private:
    uint16_t _size;
    uint16_t _offset;
    const starling_read* _sread_ptr;
};


// debugging output:
void
short_report(std::ostream& os, const read_segment& rseg);

std::ostream& operator<<(std::ostream& os, const read_segment& rseg);

#endif