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/*
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* Variant.hpp
*
* Created on: Aug 27, 2009
* Author: caa
*/
#ifndef VARIANT_HPP_
#define VARIANT_HPP_
#include <string>
#include <vector>
using namespace std;
class Variant
{
public:
Variant() {};
Variant(const string & _str) { initFromString(_str); }
int size() const { return length; };
typedef enum { INS, DEL, SNP, REF } Type;
const string & getString() const { return str; };
const string & getSeq() const { return seq; }
Type getType() const { return type; }
bool isIndel() const { if (type==INS || type==DEL) return true; else return false; };
bool isSNP() const { if (type==SNP) return true; else return false; };
bool isRef() const { if (type==REF) return true; else return false; };
protected:
void initFromString(const string & str)
{
int ok=1;
if (str.size()>1) {
if (str[0]=='-') {
// deletion
length=int(str.size())-1;
seq=str.substr(1, length);
type=Variant::DEL;
} else if (str[0]=='+') {
length=(int(str.size())-1);
seq=str.substr(1, length);
type=Variant::INS;
} else if (str.size()==4 && str[1]=='=' && str[2]=='>') {
type=Variant::SNP;
seq=str;
length=1;
} else if (str=="*REF") {
type=Variant::REF;
seq=string("*REF");
length=1;
} else ok=0;
} else ok=0;
if (!ok) { cout << "input string: " << str << endl; throw string("Unrecognized variant"); }
this->str=str;
}
Type type;
string seq;
string str;
int length;
};
class AlignedVariant : public Variant
{
public:
AlignedVariant() {};
AlignedVariant(const string & _str, int _startHap, int _endHap, int _startRead, int _endRead)
{
initFromString(_str);
startHap=_startHap;
endHap=_endHap;
startRead=_startRead;
endRead=_endRead;
leftFlankHap = startHap;
leftFlankRead = startRead;
rightFlankHap = endHap;
rightFlankRead = endRead;
freq = -1.0;
addComb = false;
}
AlignedVariant(const string & _str, int canonicalPos, double _freq=-1.0, bool _addComb = false)
{
initFromString(_str);
startHap = canonicalPos;
if (type==DEL) {
endHap = startHap+length-1;
} else {
endHap = startHap;
}
startRead=-1;
endRead = -1;
leftFlankHap = startHap;
leftFlankRead = startRead;
rightFlankHap = endHap;
rightFlankRead = endRead;
freq=_freq;
addComb = _addComb;
}
bool isCovered(int pad, int firstBase, int lastBase) const
{
if (firstBase+pad<=startRead && lastBase-pad>=endRead) return true; else return false;
}
bool operator<(const AlignedVariant & v) const
{
if (startHap!=v.startHap) return startHap<v.startHap; else return this->getString()<v.getString();
}
bool isEqual(int pos, int type, const string & str) const {
if (this->type == type && this->startHap == pos) {
if (type == AlignedVariant::SNP) {
if (str.substr(1,3)==this->str.substr(1,3)) return true; else return false;
} else {
if (type == AlignedVariant::INS) {
if (this->getString() == str) return true; else return false;
} else if (type == AlignedVariant::DEL) {
if (this->getString().size()==str.size()) return true; else return false;
}
}
} else return false;
return false;
}
int getStartRead() const { return startRead; };
int getStartHap() const { return startHap; };
int getEndHap() const { return endHap; };
double getFreq() const { return freq; };
bool getAddComb() const { return addComb; };
int getLeftFlankHap() const { return leftFlankHap; }
int getRightFlankHap() const { return rightFlankHap; }
int getLeftFlankRead() const { return leftFlankRead; }
int getRightFlankRead() const { return rightFlankRead; }
void setFlanking(int _leftFlankHap, int _rightFlankHap, int _leftFlankRead, int _rightFlankRead)
{
leftFlankRead = _leftFlankRead;
rightFlankRead = _rightFlankRead;
leftFlankHap = _leftFlankHap;
rightFlankHap = _rightFlankHap;
}
protected:
int startHap, endHap; // position of variant in the haplotype the read is aligned to.
int startRead, endRead; // position of variant in the read aligned to the haplotype
int leftFlankHap, rightFlankHap; // position of left and right base flanking the indel in the _haplotype_ (ie the target sequence)
int leftFlankRead, rightFlankRead; // position of left and right base flanking the indel in the _read_ (ie the sequence aligned to the target sequence)
double freq;
bool addComb; // add combinatorially in generation of candidate haplotypes?
};
#endif /* VARIANT_HPP_ */
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