--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/BEDTools-Version-2.14.3/src/utils/tabFile/tabFile.cpp	Thu Nov 03 10:25:04 2011 -0400
@@ -0,0 +1,99 @@
+/*****************************************************************************
+  tabFile.cpp
+
+  (c) 2009 - Aaron Quinlan
+  Hall Laboratory
+  Department of Biochemistry and Molecular Genetics
+  University of Virginia
+  aaronquinlan@gmail.com
+
+  Licensed under the GNU General Public License 2.0 license.
+******************************************************************************/
+#include "lineFileUtilities.h"
+#include "tabFile.h"
+
+/*******************************************
+Class methods
+*******************************************/
+
+// Constructor
+TabFile::TabFile(const string &tabFile)
+: _tabFile(tabFile)
+{}
+
+// Destructor
+TabFile::~TabFile(void) {
+}
+
+
+void TabFile::Open(void) {
+    if (_tabFile == "stdin") {
+        _tabStream = &cin;
+    }
+    else {
+        size_t foundPos;
+        foundPos = _tabFile.find_last_of(".gz");
+        // is this a GZIPPED TAB file?
+        if (foundPos == _tabFile.size() - 1) {
+            igzstream tabs(_tabFile.c_str(), ios::in);
+            if ( !tabs ) {
+                cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl;
+                exit (1);
+            }
+            else {
+                // if so, close it (this was just a test)
+                tabs.close();
+                // now set a pointer to the stream so that we
+                // can read the file later on.
+                _tabStream = new igzstream(_tabFile.c_str(), ios::in);
+            }
+        }
+        // not GZIPPED.
+        else {
+
+            ifstream tabs(_tabFile.c_str(), ios::in);
+            // can we open the file?
+            if ( !tabs ) {
+                cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl;
+                exit (1);
+            }
+            else {
+                // if so, close it (this was just a test)
+                tabs.close();
+                // now set a pointer to the stream so that we
+                // can read the file later on.
+                _tabStream = new ifstream(_tabFile.c_str(), ios::in);
+            }
+        }
+    }
+}
+
+
+// Close the TAB file
+void TabFile::Close(void) {
+    if (_tabFile != "stdin") delete _tabStream;
+}
+
+
+TabLineStatus TabFile::GetNextTabLine(TAB_FIELDS &tabFields, int &lineNum) {
+
+    // make sure there are still lines to process.
+    // if so, tokenize, return the TAB_FIELDS.
+    if (_tabStream->good() == true) {
+        string tabLine;
+        tabFields.reserve(20);
+
+        // parse the tabStream pointer
+        getline(*_tabStream, tabLine);
+        lineNum++;
+
+        // split into a string vector.
+        Tokenize(tabLine, tabFields);
+
+        // parse the line and validate it
+        return parseTabLine(tabFields, lineNum);
+    }
+
+    // default if file is closed or EOF
+    return TAB_INVALID;
+}