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#ifndef _BLASR_VULGAR_ALIGNMENT_PRINTER_HPP_
#define _BLASR_VULGAR_ALIGNMENT_PRINTER_HPP_
#include <string>
#include <sstream>
namespace VulgarOutput{
template <typename T_Alignment>
int CreateVulgarString(T_Alignment &alignment, std::string &vstring) {
std::stringstream vstream;
VectorIndex b;
int tGap, qGap, cGap;
if (alignment.blocks.size() == 0) {
vstring = "";
return 1;
}
for (b = 0; b < alignment.blocks.size() - 1; b++) {
tGap = (alignment.blocks[b+1].tPos
- (alignment.blocks[b].length +
alignment.blocks[b].tPos));
qGap = (alignment.blocks[b+1].qPos
- (alignment.blocks[b].length +
alignment.blocks[b].qPos));
if (tGap > 0 and qGap > 0)
cGap = abs(tGap - qGap);
else
cGap = 0;
tGap -= cGap;
qGap -= cGap;
vstream << " M " << alignment.blocks[b].length + cGap;
if (tGap > 0) {
vstream << " D " << tGap;
}
else {
vstream << " I " << qGap;
}
}
if (alignment.blocks.size() > 0) {
vstream << " M " << alignment.blocks[alignment.blocks.size() - 1].length;
}
vstring = vstream.str();
return 1;
}
template <typename T_Alignment>
void Print(T_Alignment &alignment, std::ostream &out) {
std::string vstring;
CreateVulgarString(alignment, vstring);
out << vstring;
}
}
#endif
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