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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/>.
*/
#include "HapBlock.hpp"
#include <sstream>
#include <iostream>
using namespace std;
HapBlock::HapBlock(const HapBlock & hb, uint32_t _start, uint32_t _len)
{
assert(hb.end()>=_start+_len-1);
pos0=_start;
pos1=_start+_len-1;
if (pos1<pos0) {
cout << "SMALLER" << endl;
}
type = HapBlock::NORMAL;
assert(pos1>=pos0);
haplotypes.clear();
bool found=false;
for (map<Haplotype, int>::const_iterator it=hb.haplotypes.begin();it!=hb.haplotypes.end();it++) {
Haplotype newHap=Haplotype(it->first, _start-hb.pos0, _len);
if (newHap.type==Haplotype::Ref) found=true;
map<Haplotype, int>::iterator hit=haplotypes.find(newHap);
if (hit==haplotypes.end()) {
haplotypes[newHap]=it->second;
} else {
if (newHap.type==Haplotype::Ref) hit->first.type=Haplotype::Ref;
hit->second+=it->second;
}
//haplotypes[ Haplotype(it->first, _start-hb.pos0, _len) ]+=it->second;
// += because subhaplotype may occur multiple times
}
}
void HapBlock::insert(const Haplotype & seq)
{
map<Haplotype, int>::iterator hit=haplotypes.find(seq);
if (hit==haplotypes.end()) {
haplotypes[seq]=1;
} else {
if (seq.type==Haplotype::Ref) hit->first.type=Haplotype::Ref;
hit->second++;
}
}
HapBlock::HapBlock(const Haplotype & h, uint32_t start)
{
pos0=start;
pos1=start+h.size()-1;
if (pos1<pos0) {
cout << pos0 << " " << pos1 << " " << endl;
cout << "h: " << h << endl;
}
assert(pos1>=pos0);
haplotypes[h]=1;
type=HapBlock::NORMAL;
}
void HapBlock::setFrequencies()
{
int sum=0;
for (map<Haplotype, int>::iterator it=haplotypes.begin();it!=haplotypes.end();it++) {
sum+=it->second;
}
for (map<Haplotype, int>::iterator it=haplotypes.begin();it!=haplotypes.end();it++) {
(it->first).freq=double(it->second)/double(sum);
}
}
ostream &operator<<(ostream &stream, const HapBlock &hb)
{
// construct matrix
vector<string> output(hb.length());
vector<int> counts;
vector<double> freqs;
for (map<Haplotype, int>::const_iterator it=hb.haplotypes.begin();it!=hb.haplotypes.end();it++)
{
for (size_t y=0;y<hb.length();y++) {
if ((it->first).size()>y) output[y]+=((it->first)[y]); else output[y]+='.';
output[y]+=' ';
}
counts.push_back(it->second);
freqs.push_back(it->first.freq);
}
stream << "start: " << hb.start() << " end: " << hb.end() << " numHap: " << hb.haplotypes.size() << endl;
for (size_t y=0;y<output.size();y++) cout << output[y] << endl;
for (size_t y=0;y<counts.size();y++) cout << freqs[y] << " "; cout << endl;
for (size_t y=0;y<counts.size();y++) cout << counts[y] << " "; cout << endl;
for (map<Haplotype, int>::const_iterator it=hb.haplotypes.begin();it!=hb.haplotypes.end();it++) cout << it->first.type << " ";
return stream;
}
bool HapBlock::hasHaplotype(const Haplotype & seq, uint32_t seqStart)
{
//cout << "hasHaplotype(" << seq << "," << seqStart << "): ";
for (map<Haplotype, int>::iterator it=haplotypes.begin();it!=haplotypes.end();it++) {
if (it->first.compare(seqStart-start(), seq.size(), seq)==0) { it->second++; /*cout << "true" << endl;*/ return true; };
}
//cout << "false" << endl;
return false;
}
void HapBlock::showVector(ostream &stream,const vector<HapBlock*> & hapBlocks,uint32_t midPos)
{
size_t nb=hapBlocks.size();
vector<size_t> length(nb,0), num(nb,0), pos(nb,0);
vector<HapBlock*> hbs(nb);
size_t y=0,x=0,c=0;
const size_t offset=20;
size_t indelPos=0;
for (x=0;x<nb;x++) if (hapBlocks[x]!=NULL){
pos[c]=offset+y;
if (midPos>=hapBlocks[x]->start() && midPos<=hapBlocks[x]->end()) indelPos=pos[c];
length[c]=hapBlocks[x]->length();
y+=length[c];
hbs[c]=hapBlocks[x];
num[c]=hbs[c]->size();
c++;
}
/*
for (map<int, HapBlock *>::const_iterator it=hb.insertions.begin();it!=hb.insertions.end();it++,x++) {
pos[c]=y;
length[c]=it->second->length();
y+=length[c];
hbs[c]=it->second;
num[c]=hbs[c]->size();
c++;
}
*/
size_t maxLen=*max_element(num.begin(), num.end());
vector<string> lines(maxLen*2+1,string(offset+y,' '));
lines[1][1]='R'; lines[1][2]='E'; lines[1][3]='F';
//for (size_t x=0;x<lines.size();x++) { lines[x][0]='\t'; };
for (size_t i=0;i<pos.size();i++) {
//cout << "o: " << o << " o.size() : " << o.size() << " pos[i]: " << pos[i] << endl;
lines[0][pos[i]]='|';
/*
size_t j=1;
for (map<Haplotype, int>::const_iterator it=hbs[i]->haplotypes.begin();it!=hbs[i]->haplotypes.end();it++) {
string u=it->first.seq;
//cout << "u: " << u << endl;
for (size_t l=0;l<u.size();l++) lines[j][pos[i]+l]=u[l];
j++;
}
j=maxLen+1;
for (map<Haplotype, int>::const_iterator it=hbs[i]->haplotypes.begin();it!=hbs[i]->haplotypes.end();it++) {
string o;
ostringstream os(ostringstream::out);
os << int(round(-log(it->first.freq))); o=os.str();
for (size_t l=0;l<o.size();l++) lines[j][pos[i]+l]=o[l];
j++;
}
*/
// order haplotypes such that reference sequence is top, then sorted based on frequency
vector<Haplotype> haps; Haplotype refHap;
for (map<Haplotype, int>::const_iterator it=hbs[i]->haplotypes.begin();it!=hbs[i]->haplotypes.end();it++) if (it->first.type!=Haplotype::Ref) haps.push_back(it->first); else refHap=it->first;
class SortFunc
{
public:
static bool sortFunc(const Haplotype & h1, const Haplotype & h2) { return h1.freq<h2.freq; };
};
sort(haps.begin(),haps.end(), SortFunc::sortFunc);
haps.push_back(refHap);
size_t j=1;
for (int k=int(haps.size())-1;k>=0;k--) {
string u=haps[k].seq;
//cout << "u: " << u << endl;
for (size_t l=0;l<u.size();l++) lines[j][pos[i]+l]=u[l];
j++;
}
j=maxLen+1;
for (int k=int(haps.size())-1;k>=0;k--) {
string o;
ostringstream os(ostringstream::out);
os << int(round(-log(haps[k].freq))); o=os.str();
for (size_t l=0;l<o.size();l++) lines[j][pos[i]+l]=o[l];
j++;
}
}
lines[0][indelPos]='X';
for (size_t j=0;j<lines.size();j++) {
stream << lines[j] << endl;
}
}
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