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#include "SeqLib/STCoverage.h"
#include "SeqLib/SeqLibCommon.h"
#include <stdexcept>
#include <algorithm>
namespace SeqLib {
void STCoverage::clear() {
m_map.clear();
}
void STCoverage::settleCoverage() {
GRC tmp = m_grc;
m_grc.mergeOverlappingIntervals();
}
STCoverage::STCoverage(const SeqLib::GenomicRegion& gr) {
m_gr = gr;
v = uint16_sp(new std::vector<uint16_t>(gr.width(),0));
}
uint16_t STCoverage::maxCov() const {
return (*std::max_element(v->begin(), v->end()));
}
/*void STCoverage::addRead2(const BamRecord& r) {
int p = r.Position();
int e = r.PositionEnd();
if (p < 0 || e < 0)
return;
if (p < m_gr.pos1 || e > m_gr.pos2)
return;
if (r.ChrID() != m_gr.chr)
return;
assert(p - m_gr.pos1 < v->size());
++v[p - m_gr.pos1];
}
*/
void STCoverage::addRead(const BamRecord &r, int buff, bool full_length) {
//m_settled = false;
//m_grc.add(GenomicRegion(r.ChrID(), r.Position(), r.PositionEnd()));
// out of bounds
//if (r.Position() < m_gr.pos1 || r.PositionEnd() > m_gr.pos2 || r.ChrID() != m_gr.chr)
// return;
//int p = std::min(r.Position() - m_gr.pos1, m_gr.pos2);
//int e = std::min(r.PositionEnd() - m_gr.pos1, m_gr.pos2);
int p = -1;
int e = -1;
if (full_length) {
Cigar c = r.GetCigar();
// get beginning
if (c.size() && c[0].RawType() == BAM_CSOFT_CLIP)
p = std::max((int32_t)0, r.Position() - (int32_t)c[0].Length()); // get prefixing S
else
p = r.Position();
// get end
if (c.size() && c.back().RawType() == BAM_CSOFT_CLIP)
e = r.PositionEnd() + c.back().Length();
else
e = r.PositionEnd();
}
else {
p = r.Position() + buff;
e = r.PositionEnd() - buff;
}
if (p < 0 || e < 0)
return;
// if we don't have an empty map for this, add
if (r.ChrID() >= (int)m_map.size()) {
int k = m_map.size();
while (k <= r.ChrID()) {
m_map.push_back(CovMap());
//m_map.back().reserve(reserve_size);
++k;
}
}
assert(e - p < 1e6); // limit on read length
assert(r.ChrID() >= 0);
assert(r.ChrID() < (int)m_map.size());
try {
while (p <= e) {
//CovMap::iterator iter = m_map.find(p);
++(m_map[r.ChrID()][p]); // add one to this position
++p;
//if (v->at(p) < 60000) // 60000 is roughly int16 lim
// v->at(p)++;
//++p;
}
} catch (std::out_of_range &oor) {
std::cerr << "Position " << p << " on tid " << r.ChrID()
<< " is greater than expected max of " << v->size() << " -- skipping" << std::endl;
}
}
std::ostream& operator<<(std::ostream &out, const STCoverage &c) {
out << "Region " << c.m_gr << " v.size() " << c.v->size() << std::endl;
return out;
}
void STCoverage::ToBedgraph(std::ofstream * o, const bam_hdr_t * h) const {
//settleCoverage();
// unitialized so nothing to do
if (m_gr.chr == -1 || v->size() == 0)
return;
size_t curr_start = 0;
size_t curr_val = v->at(0);
for (size_t i = 0; i < v->size(); ++i) {
if (v->at(i) != curr_val) {
(*o) << m_gr.ChrName(h) << "\t" << (curr_start + m_gr.pos1) << "\t" << (i+m_gr.pos1) << "\t" << curr_val << std::endl;
curr_start = i;
curr_val = v->at(i);
}
}
// need to dump last one
if ( (curr_start+1) != v->size())
(*o) << m_gr.ChrName(h) << "\t" << (curr_start + m_gr.pos1) << "\t" << (v->size()+m_gr.pos1-1) << "\t" << curr_val << std::endl;
}
int STCoverage::getCoverageAtPosition(int chr, int pos) const {
//CovMapMap::iterator it = m_map.find(chr);
//if (it == m_map.end())
// return 0;
if (chr >= (int)m_map.size())
return 0;
//std::cerr << " MAP " << std::endl;
//for (auto& i : m_map)
// std::cerr << i.first << " " << i.second << std::endl;
//if (!m_settled)
// settleCoverage();
//if (pos < m_gr.pos1 || pos > m_gr.pos2) {
//std::cerr << "Coverage query out of bounds for location " << m_gr.chr << ":" << pos << std::endl;
// return 0;
//}
//size_t q = pos - m_gr.pos1;
//if (q >= v->size()) {
// std::cerr << "Coverage query out of bounds for location " << m_gr.chr << ":" << pos << " with pos-start of " << q << " attempt on v of size " << v->size() << std::endl;
// return 0;
//}
//return it->second[pos];
CovMap::const_iterator ff = m_map[chr].find(pos);
if (ff == m_map[chr].end()) {
return 0;
}
return ff->second;
//return (v->at(q));
}
}
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