// -*- 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 __INDEL_UTIL_HH
#define __INDEL_UTIL_HH

#include "indel.hh"
#include "depth_buffer.hh"
#include "blt_util/pos_range.hh"
#include "starling/starling_shared.hh"


// do these two indels overlap?:
bool
is_indel_conflict(const indel_key& ik1,
                  const indel_key& ik2);

bool
is_range_intersect_indel_breakpoints(const known_pos_range read_pr,
                                     const indel_key& ik);

// is an indel treated as a candidate for genotype calling and
// realignment or as a "private" (ie. noise) indel?
//
inline
bool
is_candidate_indel(const starling_options& client_opt,
                   const depth_buffer& db,
                   const indel_key& ik,
                   const indel_data& id){

    if(not id.is_candidate_indel_cached) {
        const int n_reads(static_cast<int>(id.all_read_ids.size()));
        const bool is_min_reads(n_reads >=  client_opt.min_candidate_indel_reads);

        // note estdepth is based on genomic reads only, so readfrac can be > 1:
        //
        static const unsigned one(1); // <- get around type-mismatch error in std::max() below
        const unsigned estdepth(std::max(one,db.val(ik.pos-1)));
        const double readfrac(static_cast<double>(n_reads)/static_cast<double>(estdepth));

        double min_frac(client_opt.min_candidate_indel_read_frac);
        if(static_cast<int>(ik.length) <= client_opt.max_small_candidate_indel_size) {
            min_frac=std::max(min_frac,client_opt.min_small_candidate_indel_read_frac);
        }
        const bool is_min_frac(readfrac >= min_frac);
        id.is_candidate_indel=(is_min_reads and is_min_frac);
        id.is_candidate_indel_cached=true;
    }
    return id.is_candidate_indel;
}


// is an indel either a candidate indel or in at least one of the
// discovery alignments for this read?
//
inline
bool
is_usable_indel(const starling_options& client_opt,
                const depth_buffer& db,
                const indel_key& ik,
                const indel_data& id,
                const align_id_t read_id){

    return (is_candidate_indel(client_opt,db,ik,id) or
            (id.all_read_ids.count(read_id)>0) or
            (id.submap_read_ids.count(read_id)>0));
}


#endif