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/* The MIT License
Copyright (c) 2013 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.
*/
#include "hts_utils.h"
#include "utils.h"
#include "allele.h"
#include "vntr.h"
#ifndef VARIANT_H
#define VARIANT_H
/**
* This represents a Variant and is augmented on top of VCF's record to handle the notion of variants as defined by us.
*
* This turned out to be a really heavy class. Some notes:
*
* 1. Augmented record of a variant on top of a VCF record
* 2. Has tandem repeat specific properties in the class VNTR
* 3. Links to overlapping VCF records to aid making multiallelics
*
* This class is NOT responsible for the destruction of ANY bcf records.
*/
class Variant
{
public:
//aggegrated type from the alleles
int32_t type;
//location information
std::string chrom;
uint32_t rid;
int32_t pos1; //position of first reference base in VCF record
int32_t beg1; //same as pos1
int32_t end1; //same as end1
//linked VCF record
bcf_hdr_t* h;
bcf1_t* v;
//associated VCF records for merging into a multiallelic
std::vector<bcf1_t*> vs;
std::vector<bcf1_t*> snp_vs;
std::vector<bcf1_t*> indel_vs;
std::vector<bcf1_t*> vntr_vs;
std::vector<bcf1_t*> consolidated_vntr_vs;
//contains alleles
std::vector<Allele> alleles;
//sum from all the alleles
int32_t ts; //no. of transitions
int32_t tv; //no. of tranversions (mlen-ts)
int32_t ins; //no. of insertions
int32_t del; //no. of deletions
int32_t max_dlen; //maximum allele length difference
int32_t min_dlen; //minimum allele length difference
//overlapping statistics
//for normal variants
// - the number of other variants overlapping with this
//for candidate multiallelic/complex variant
// - the number of variants considered for merging into a multiallelic/complex variant
int32_t no_overlapping_snps;
int32_t no_overlapping_indels;
int32_t no_overlapping_vntrs;
bool is_new_multiallelic;
bool is_involved_in_a_multiallelic;
Variant* associated_new_multiallelic;
bool updated_multiallelic;
//describes VNTR
VNTR vntr;
//contains N bases in alleles
bool contains_N;
/**
* Constructor.
*/
Variant(bcf_hdr_t* h, bcf1_t* v);
/**
* Constructor for a variant object that is to be composed from several variants.
* ??????? WHY DO THIS????????
*/
Variant(Variant* v1, Variant* v2);
/**
* Constructor.
*/
Variant();
/**
* Destructor.
*/
~Variant();
/**
* Clears variant information.
*/
void clear();
/**
* Classifies variants based on observed alleles in vcf record.
*/
int32_t classify(bcf_hdr_t *h, bcf1_t *v);
/**
* Updates VNTR related information from INFO fields.
*/
void update_vntr_from_info_fields();
/**
* Updates VNTR related information from INFO fields.
*/
void update_vntr_from_info_fields(bcf_hdr_t *h, bcf1_t *v);
/**
* Updates a bcf1_t object with VNTR information.
*/
void update_bcf_with_vntr_info(bcf_hdr_t *h, bcf1_t *v);
/**
* Prints variant information.
*/
void print();
/**
* Gets a string representation of the variant.
*/
std::string get_variant_string();
/**
* Gets a string representation of the underlying VNTR by exact alignment.
*/
void get_vntr_string(kstring_t* s);
/**
* Gets a string representation of the underlying VNTR by fuzzy alignment.
*/
void get_fuzzy_vntr_string(kstring_t* s);
/**
* Converts VTYPE to string.
*/
static std::string vtype2string(int32_t VTYPE);
};
#endif
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