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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/>.
*/
/*
* MLAlignment.hpp
*
* Created on: Apr 2, 2009
* Author: caa
*/
#ifndef MLALIGNMENT_HPP_
#define MLALIGNMENT_HPP_
#include <vector>
#include <string>
#include <map>
#include "Variant.hpp"
class MLAlignment
{
public:
static const int INS=-1;
static const int DEL=-2;
static const int LO=-3;
static const int RO=-4;
MLAlignment()
{
relPos=-1;
ll=0.0;
llOn=0.0;
llOff=0.0;
offHap=false;
offHapHMQ=false;
numIndels=0;
numMismatch=0;
hr=-1;
hl=-1;
}
int relPos; // relative position of read wrt haplotype
int firstBase, lastBase; //first and last base of haplotype covered by the read
map<int, AlignedVariant> indels, snps;
map<int, bool> hapIndelCovered, hapSNPCovered; // indels and snps in the _haplotype_ covered by the read
double ll; // loglikelihood
double llOn, llOff; // without priors/mapping qualities taken into account
bool offHap, offHapHMQ; // haplotype is mapped outside haplotype window with read-mapping quality and an artificial high-mapping-quality respectively
int hl, hr; // left and rightmost base on haplotype covered by the read
int numIndels, numMismatch;
int nBQT, nmmBQT; // number of aligned bases and number mismatching above threshold
double mLogBQ; // mean log BaseQuality
int nMMLeft, nMMRight;
string align;
vector<int> hpos;
operator double() const { return ll; };
void print()
{
cout << "relPos: " << relPos << " offHap: " << (int) offHap << " ll: " << ll << endl;
}
};
#endif /* MLALIGNMENT_HPP_ */
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