--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/utils/bedGraphFile/bedGraphFile.h	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,199 @@
+/*****************************************************************************
+  bedGraphFile.cpp
+
+  (c) 2010 - Assaf Gordon
+  Hall Laboratory
+  Department of Biochemistry and Molecular Genetics
+  University of Virginia
+  aaronquinlan@gmail.com
+
+  Licenced under the GNU General Public License 2.0 license.
+******************************************************************************/
+#ifndef BEDGRAPHFILE_H
+#define BEDGRAPHFILE_H
+
+#include "gzstream.h"
+#include "lineFileUtilities.h"
+#include "fileType.h"
+#include <vector>
+#include <map>
+#include <set>
+#include <string>
+#include <iostream>
+#include <fstream>
+#include <sstream>
+#include <cstring>
+#include <algorithm>
+#include <limits.h>
+#include <stdint.h>
+#include <cstdio>
+
+using namespace std;
+
+//*************************************************
+// Data type tydedef
+//*************************************************
+#ifndef CHRPOS
+typedef uint32_t CHRPOS;
+#endif
+
+#ifndef DEPTH
+typedef uint32_t DEPTH;
+#endif
+
+/*
+   Structure for regular BedGraph records
+ */
+template <typename T>
+class BEDGRAPH
+{
+public:
+    std::string chrom;
+    CHRPOS start;
+    CHRPOS end;
+    T depth;
+
+public:
+    typedef T DEPTH_TYPE;
+    // constructors
+
+    // Null
+    BEDGRAPH() :
+        start(0),
+        end(0),
+        depth(T())
+    {}
+
+    // BEDGraph
+    BEDGRAPH(string _chrom, CHRPOS _start, CHRPOS _end, T _depth) :
+        chrom(_chrom),
+        start(_start),
+        end(_end),
+        depth(_depth)
+    {}
+}; // BEDGraph
+
+typedef BEDGRAPH<int32_t> BEDGRAPH_INT;
+typedef BEDGRAPH<std::string> BEDGRAPH_STR;
+typedef BEDGRAPH<double> BEDGRAPH_FLOAT;
+
+template <typename T>
+std::ostream& operator<< (std::ostream& strm, const BEDGRAPH<T>& bg)
+{
+    strm << bg.chrom << "\t"
+        << bg.start << "\t"
+        << bg.end << "\t"
+        << bg.depth;
+    return strm;
+}
+
+// enum to flag the state of a given line in a BEDGraph file.
+enum BedGraphLineStatus
+{
+    BEDGRAPH_INVALID = -1,
+    BEDGRAPH_HEADER  = 0,
+    BEDGRAPH_BLANK   = 1,
+    BEDGRAPH_VALID   = 2
+};
+
+
+//************************************************
+// 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);
+
+            // 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;
+
+    template <typename T>
+    BedGraphLineStatus parseLine (BEDGRAPH<T> &bg, const vector<string> &lineVector, int &lineNum)
+    {
+        if (lineVector.size() == 0)
+            return BEDGRAPH_BLANK;
+
+        if (lineVector[0].find("track")   != string::npos ||
+            lineVector[0].find("browser") != string::npos ||
+            lineVector[0].find("#") != string::npos)
+            return BEDGRAPH_HEADER;
+
+        if (lineVector.size() != 4)
+            return BEDGRAPH_INVALID;
+
+        bg.chrom = lineVector[0];
+
+        stringstream str_start(lineVector[1]);
+        if (! (str_start >> bg.start) ) {
+            cerr << "Input error, failed to extract start value from '" << lineVector[1]
+                << "' (column 2) in " << bedGraphFile << " line " << lineNum << endl;
+            exit(1);
+        }
+
+        stringstream str_end(lineVector[2]);
+        if (! (str_end >> bg.end) ) {
+            cerr << "Input error, failed to extract end value from '" << lineVector[2]
+                << "' (column 3) in " << bedGraphFile << " line " << lineNum << endl;
+            exit(1);
+        }
+
+        stringstream str_depth(lineVector[3]);
+        if (! (str_depth >> bg.depth) ) {
+            cerr << "Input error, failed to extract depth value from '" << lineVector[3]
+                << "' (column 4) in " << bedGraphFile << " line " << lineNum << endl;
+            exit(1);
+        }
+
+        return BEDGRAPH_VALID;
+    }
+};
+
+#endif /* BEDFILE_H */