Added gzstream to bedFile.

src/utils/bedFile/bedFile.cpp

@@ -181,8 +181,8 @@ bool BedFile::GetNextBed (BED &bed, int &lineNum) {
 		if (parseLine(bed, bedFields, lineNum)) {
 			return true;
 		}
-		return false;
 	}
+	return false;
 }
 
 
@@ -355,22 +355,6 @@ void BedFile::countHits(const BED &a, bool forceStrand) {
 }
 
 
-
-
-/*******************************************
-Class methods
-*******************************************/
-
-// Constructor
-BedFile::BedFile(string &bedFile) {
-	this->bedFile = bedFile;
-}
-
-// Destructor
-BedFile::~BedFile(void) {
-}
-
-
 void BedFile::setGff (bool gff) {
 	if (gff == true) this->isGff = true;
 	else this->isGff = false;

src/utils/bedFile/bedFile.h

@@ -12,6 +12,7 @@
 #ifndef BEDFILE_H
 #define BEDFILE_H
 
+#include "gzstream.h"
 #include <vector>
 #include <map>
 #include <string>
@@ -22,7 +23,7 @@
 #include <algorithm>
 #include <limits.h>
 #include <cstdio>
-//#include <tr1/unordered_map>
+
 using namespace std;
 
 //*************************************************
@@ -207,6 +208,8 @@ private:
 	bool parseGffLine (BED &bed, const vector<string> &lineVector, int lineNum);
 	
 	void setGff (bool isGff);
+	
+	istream *bedStream;
 };
 
 #endif /* BEDFILE_H */