vntr.h

/* The MIT License

   Copyright (c) 2015 Adrian Tan <atks@umich.edu>

   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
   in the Software without restriction, including without limitation the rights
   to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
   copies of the Software, and to permit persons to whom the Software is
   furnished to do so, subject to the following conditions:

   The above copyright notice and this permission notice shall be included in
   all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
   IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
   FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
   AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
   LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
   OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
   THE SOFTWARE.
*/

#ifndef VNTR_H
#define VNTR_H

#include <cstdlib>
#include <stdint.h>
#include <string>
#include <cmath>
#include <cfloat>
#include <vector>
#include <iostream>

/**
 * Class for representing a VNTR.
 *
 * 2 sets of attributes for the exact and fuzzy detections of the repeat region.
 */
class VNTR
{
    public:

    //chromosome
    int32_t rid;  //rid, redundant data with Variant. todo: something about this.

    //motif
    std::string motif;         //motif
    std::string ru;            //repeat unit on the reference
    uint32_t mlen;             //length of motif
    float motif_score;         //motif score from motif tree

    //exact repeat tract
    std::string repeat_tract;   //repeat tract
    int32_t rbeg1;              //beginning of repeat tract
    int32_t rend1;              //end of repeat tract
    float rl;                   //number of repeat units on repeat tract
    float ll;                   //number of repeat units on longest allele
    float motif_concordance;    //motif concordance from hmm
    int32_t no_exact_ru;        //number exact repeat units from hmm
    int32_t total_no_ru;        //total no of repeat units from hmm
    std::string lflank;         //left flank
    std::string rflank;         //right flank

    //fuzzy repeat tract
    std::string fuzzy_repeat_tract;   //repeat tract
    int32_t fuzzy_rbeg1;              //beginning of repeat tract
    int32_t fuzzy_rend1;              //end of repeat tract
    float fuzzy_rl;                   //number of repeat units on repeat tract
    float fuzzy_ll;                   //number of repeat units on longest allele
    float fuzzy_motif_concordance;    //motif concordance from hmm
    int32_t fuzzy_no_exact_ru;        //number exact repeat units from hmm
    int32_t fuzzy_total_no_ru;        //total no of repeat units from hmm
    std::string fuzzy_lflank;         //left flank
    std::string fuzzy_rflank;         //right flank

    //large repeat tract
    bool is_large_repeat_tract;

    /**
     * Constructor.
     */
    VNTR();

    /**
     * Clear object.
     */
    void clear();

    /**
     * Checks for equality.
     */
    bool equals(VNTR& vntr);

    /**
     * Get VNTR representation in string format.
     */
    void get_vntr_allele_string(std::string& var);

    /**
     * Get VNTR fuzzy representation in string format.
     */
    void get_fuzzy_vntr_allele_string(std::string& var);

    /**
     * Print object.
     */
    void print();
};
#endif