Class BedGraphFile

src/utils/bedGraphFile/bedGraphFile.h:103–200

BedGraphFile Class methods and elements

// BedGraphFile Class methods and elements
//************************************************
class BedGraphFile {

public:

    // Constructor
    BedGraphFile(string &);

    // Destructor
    ~BedGraphFile(void);

    // Open a BEDGraph file for reading (creates an istream pointer)
    void Open(void);

    // Close an opened BED file.
    void Close(void);

    // Get the next BED entry in an opened BED file.
    template <typename T>
    BedGraphLineStatus GetNextBedGraph (BEDGRAPH<T> &bedgraph, int &lineNum)
    {
        // make sure there are still lines to process.
        // if so, tokenize, validate and return the BED entry.
        if (_bedGraphStream->good()) {
            string bedGraphLine;
            vector<string> bedGraphFields;

            // parse the bedStream pointer
            getline(*_bedGraphStream, bedGraphLine);
            if (_bedGraphStream->eof())
                return BEDGRAPH_INVALID;
            if (_bedGraphStream->bad()) {
                cerr << "Error while reading file '" << bedGraphFile << "' : "
                    << strerror(errno) << endl;
                exit(1);
            }
            lineNum++;

            // split into a string vector.
            Tokenize(bedGraphLine,bedGraphFields);
            if (bedGraphLine[bedGraphLine.size()-1] == '\r') {
                bedGraphLine.resize(bedGraphLine.size()-1);
            }

            // load the BED struct as long as it's a valid BED entry.
            return parseLine(bedgraph, bedGraphFields, lineNum);
        }

        // default if file is closed or EOF
        return BEDGRAPH_INVALID;
    }

    // the bedfile with which this instance is associated
    string bedGraphFile;

private:
    // data
    istream *_bedGraphStream;