Version 2.1.1

	1. Added limits.h to bedFile.h to prevent compilation errors on some systems.
	2. Fixed the bedFile.cpp parsing logic to allow proper parsing of track and browser lines

src/utils/bedFile/bedFile.cpp

@@ -376,12 +376,11 @@ void BedFile::loadBedFileIntoMapNoBin() {
 
 		while (getline(bed, bedLine)) {
 
-			if ((bedLine.find_first_of("track") == 1) || (bedLine.find_first_of("browser") == 1)) {
+			if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
 				continue;
 			}
 			else {
 				Tokenize(bedLine,bedFields);
-
 				lineNum++;
 
 				if (parseBedLine(bedEntry, bedFields, lineNum)) {
@@ -398,7 +397,7 @@ void BedFile::loadBedFileIntoMapNoBin() {
 				
 		while (getline(cin, bedLine)) {
 
-			if ((bedLine.find_first_of("track") == 1) || (bedLine.find_first_of("browser") == 1)) {
+			if ((bedLine.find("track") != string::npos) || (bedLine.find("browser") != string::npos)) {
 				continue;
 			}
 			else {

src/utils/bedFile/bedFile.h

@@ -9,6 +9,7 @@
 #include <sstream>
 #include <cstring>
 #include <algorithm>
+#include <limits.h>
 
 using namespace std;
 

src/utils/lineFileUtilities/lineFileUtilities.cpp

@@ -9,8 +9,6 @@
 //
 
 #include "lineFileUtilities.h"
-
-
 //***********************************************
 // lineFileUtilities:
 // 		Common Functions
@@ -18,6 +16,20 @@
 
 void Tokenize(const string& str, vector<string>& tokens)
 {
+
+/*
+	string::size_type start = 0;
+	string::size_type end = 0;
+
+	cout << str << endl; 
+	while ((start = str.find_first_not_of(" ", start)) != string::npos) {
+	    end = str.find_first_of(" ", start);
+		cout << start << ":" << end << endl;
+	    tokens.push_back(str.substr(start, end - start));
+	    start = end;
+	  }
+*/
+
 	// Skip delimiters at beginning.
 	string::size_type lastPos = str.find_first_not_of("\t", 0);
 	// Find first "non-delimiter".
@@ -32,6 +44,7 @@ void Tokenize(const string& str, vector<string>& tokens)
 		// Find next "non-delimiter"
 		pos = str.find_first_of("\t", lastPos);
 	}
+
 }
 
 

src/utils/lineFileUtilities/lineFileUtilities.h

@@ -5,6 +5,7 @@
 #include <string>
 #include <algorithm>
 
+
 using namespace std;
 
 // split a line from a file into a vector of strings.  token = "\t"