exit is inout BAM file is not found

src/coverageBed/coverageBed.cpp

@@ -85,10 +85,12 @@ void BedCoverage::CollectCoverageBam(string bamFile) {
     // that we can easily compare "A" to it for overlaps
     _bedB->loadBedCovFileIntoMap();
 
-    // open the BAM file
+    // open the BAM file		
     BamReader reader;
-    reader.Open(bamFile);
-
+    if (!reader.Open(bamFile)) {
+        cerr << "Failed to open BAM file " << bamFile << endl;
+        exit(1);
+    }
     // get header & reference information
     string header = reader.GetHeaderText();
     RefVector refs = reader.GetReferenceData();

src/genomeCoverageBed/genomeCoverageBed.cpp

@@ -211,7 +211,10 @@ void BedGenomeCoverage::CoverageBam(string bamFile) {
 
     // open the BAM file
     BamReader reader;
-    reader.Open(bamFile);
+    if (!reader.Open(bamFile)) {
+        cerr << "Failed to open BAM file " << bamFile << endl;
+        exit(1);
+    }
 
     // get header & reference information
     string header = reader.GetHeaderText();

src/intersectBed/intersectBed.cpp

@@ -308,7 +308,11 @@ void BedIntersect::IntersectBam(string bamFile) {
     // open the BAM file
     BamReader reader;
     BamWriter writer;
-    reader.Open(bamFile);
+    if (!reader.Open(bamFile)) {
+        cerr << "Failed to open BAM file " << bamFile << endl;
+        exit(1);
+    }
+    
     // get header & reference information
     string bamHeader  = reader.GetHeaderText();
     RefVector refs    = reader.GetReferenceData();

src/pairToBed/pairToBed.cpp

@@ -383,7 +383,10 @@ void BedIntersectPE::IntersectBamPE(string bamFile) {
     // open the BAM file
     BamReader reader;
     BamWriter writer;
-    reader.Open(bamFile);
+    if (!reader.Open(bamFile)) {
+        cerr << "Failed to open BAM file " << bamFile << endl;
+        exit(1);
+    }
 
     // get header & reference information
     string bamHeader = reader.GetHeaderText();

src/tagBam/tagBam.cpp

@@ -64,7 +64,11 @@ void TagBam::Tag() {
     // open the BAM file
     BamReader reader;
     BamWriter writer;
-    reader.Open(_bamFile);
+	if (!reader.Open(_bamFile)) {
+        cerr << "Failed to open BAM file " << _bamFile << endl;
+        exit(1);
+    }
+    
     // get header & reference information
     string bamHeader  = reader.GetHeaderText();
     RefVector refs = reader.GetReferenceData();

src/utils/chromsweep/chromsweep.cpp

@@ -169,9 +169,9 @@ bool ChromSweep::Next(pair<BED, vector<BED> > &next) {
             {
                 if (IsValidHit(_curr_qy, _curr_db)) {
                     _hits.push_back(_curr_db);
-                }
-                _cache.push_back(_curr_db);
-                _db->GetNextBed(_curr_db, true);
+				}
+				_cache.push_back(_curr_db);
+				_db->GetNextBed(_curr_db, true);
             }
             // add the hits for this query to the pump
             _results.push(make_pair(_curr_qy, _hits));

src/windowBed/windowBed.cpp

@@ -158,7 +158,11 @@ void BedWindow::WindowIntersectBam(string bamFile) {
     // open the BAM file
     BamReader reader;
     BamWriter writer;
-    reader.Open(bamFile);
+    if (!reader.Open(bamFile)) {
+        cerr << "Failed to open BAM file " << bamFile << endl;
+        exit(1);
+    }
+
 
     // get header & reference information
     string bamHeader  = reader.GetHeaderText();