bedtools patch to accomodate empty files

empty_file.patch

diff -rupN bedtools-master/src/utils/bedFile/bedFile.cpp bedtools-master-jp/src/utils/bedFile/bedFile.cpp
--- bedtools-master/src/utils/bedFile/bedFile.cpp	2012-11-05 03:48:10.000000000 -0800
+++ bedtools-master-jp/src/utils/bedFile/bedFile.cpp	2012-11-09 13:52:15.000000000 -0800
@@ -101,7 +101,7 @@ void BedFile::Open(void) {
             delete _bedStream;
             _bedStream = new igzstream(bedFile.c_str(), ios::in);
         }
-        if ( !(_bedStream->good()) ) {
+        if ( (_bedStream->bad()) ) {
             cerr << "Error: The requested bed file (" 
                  << bedFile 
                  << ") could not be opened. Exiting!" << endl;
diff -rupN bedtools-master/src/utils/bedFilePE/bedFilePE.cpp bedtools-master-jp/src/utils/bedFilePE/bedFilePE.cpp
--- bedtools-master/src/utils/bedFilePE/bedFilePE.cpp	2012-11-05 03:48:10.000000000 -0800
+++ bedtools-master-jp/src/utils/bedFilePE/bedFilePE.cpp	2012-11-09 13:52:25.000000000 -0800
@@ -36,7 +36,7 @@ void BedFilePE::Open(void) {
             _bedStream = new igzstream(bedFile.c_str(), ios::in);
         }
         // can we open the file?
-        if ( !(_bedStream->good()) ) {
+        if ( (_bedStream->bad()) ) {
             cerr << "Error: The requested bed file (" << bedFile << ") could not be opened. Exiting!" << endl;
             exit (1);
         }
diff -rupN bedtools-master/src/utils/bedGraphFile/bedGraphFile.cpp bedtools-master-jp/src/utils/bedGraphFile/bedGraphFile.cpp
--- bedtools-master/src/utils/bedGraphFile/bedGraphFile.cpp	2012-11-05 03:48:10.000000000 -0800
+++ bedtools-master-jp/src/utils/bedGraphFile/bedGraphFile.cpp	2012-11-09 13:52:41.000000000 -0800
@@ -38,7 +38,7 @@ void BedGraphFile::Open() {
             _bedGraphStream = new igzstream(bedGraphFile.c_str(), ios::in);
         }
         // can we open the file?
-        if ( !(_bedGraphStream->good()) ) {
+        if ( (_bedGraphStream->bad()) ) {
             cerr << "Error: The requested bed file (" << bedGraphFile << ") could not be opened. Exiting!" << endl;
             exit (1);
         }
diff -rupN bedtools-master/src/utils/tabFile/tabFile.cpp bedtools-master-jp/src/utils/tabFile/tabFile.cpp
--- bedtools-master/src/utils/tabFile/tabFile.cpp	2012-11-05 03:48:10.000000000 -0800
+++ bedtools-master-jp/src/utils/tabFile/tabFile.cpp	2012-11-09 13:52:54.000000000 -0800
@@ -36,7 +36,7 @@ void TabFile::Open(void) {
             delete _tabStream;
             _tabStream = new igzstream(_tabFile.c_str(), ios::in);
         }
-        if ( !(_tabStream->good()) ) {
+        if ( (_tabStream->bad()) ) {
             cerr << "Error: The requested file (" << _tabFile << ") could not be opened. Exiting!" << endl;
             exit (1);
         }