region.cpp

#include "region.hpp"

namespace vg {

void parse_region(
    string& region,
    string& startSeq,
    int& startPos,
    int& stopPos) {

    size_t foundFirstColon = region.find(":");

    // we only have a single string, use the whole sequence as the target
    if (foundFirstColon == string::npos) {
        startSeq = region;
        startPos = 0;
        stopPos = -1;
    } else {
        startSeq = region.substr(0, foundFirstColon);
        string sep = "..";
        size_t foundRangeSep = region.find(sep, foundFirstColon);
        if (foundRangeSep == string::npos) {
            sep = "-";
            foundRangeSep = region.find("-", foundFirstColon);
        }
        if (foundRangeSep == string::npos) {
            startPos = atoi(region.substr(foundFirstColon + 1).c_str());
            // differ from bamtools in this regard, in that we process only
            // the specified position if a range isn't given
            stopPos = startPos + 1;
        } else {
            startPos = atoi(region.substr(foundFirstColon + 1, foundRangeSep - foundFirstColon).c_str());
            // if we have range sep specified, but no second number, read to the end of sequence
            if (foundRangeSep + sep.size() != region.size()) {
                stopPos = atoi(region.substr(foundRangeSep + sep.size()).c_str()); // end-exclusive, bed-format
            } else {
                //stopPos = reference.sequenceLength(startSeq);
                stopPos = -1;
            }
        }
    }
}

}