X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Ftoolkit%2Fbamtools_coverage.cpp;h=748f51337f778991c9ad724ce0e9ae6b8fad6c4a;hb=8c80d760637f8df39262683cd2570f0589423d36;hp=5924edb78a85b93af928f56610dd0b9d8be2a007;hpb=9e7f3168db0c2473674f33a66eb63dedba0353f8;p=bamtools.git

diff --git a/src/toolkit/bamtools_coverage.cpp b/src/toolkit/bamtools_coverage.cpp
index 5924edb..748f513 100644
--- a/src/toolkit/bamtools_coverage.cpp
+++ b/src/toolkit/bamtools_coverage.cpp
@@ -3,21 +3,23 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 16 September 2010
+// Last modified: 21 March 2011
 // ---------------------------------------------------------------------------
 // Prints coverage data for a single BAM file 
 // ***************************************************************************
 
+#include "bamtools_coverage.h"
+
+#include <api/BamReader.h>
+#include <utils/bamtools_options.h>
+#include <utils/bamtools_pileup_engine.h>
+using namespace BamTools;
+
 #include <iostream>
 #include <fstream>
 #include <string>
 #include <vector>
-#include "bamtools_coverage.h"
-#include "bamtools_options.h"
-#include "bamtools_pileup_engine.h"
-#include "BamReader.h"
 using namespace std;
-using namespace BamTools; 
   
 namespace BamTools {
  
@@ -36,12 +38,8 @@ class CoverageVisitor : public PileupVisitor {
   
     // PileupVisitor interface implementation
     public:
-//         void Visit(const int& refId, const int& position, const vector<BamAlignment>& alignments) {
+	// prints coverage results ( tab-delimited )
         void Visit(const PileupPosition& pileupData) {
-            // -----------------------------------------
-            // print coverage results ( tab-delimited )
-            // <refName> <0-based pos> <number of alleles>
-//             *m_out << m_references[refId].RefName << "\t" << position << "\t" << alignments.size() << endl;
             *m_out << m_references[pileupData.RefId].RefName << "\t" 
                    << pileupData.Position << "\t" 
                    << pileupData.PileupAlignments.size() << endl;
@@ -113,7 +111,8 @@ bool CoverageTool::CoverageToolPrivate::Run(void) {
         // open output file stream
         outFile.open(m_settings->OutputFilename.c_str());
         if ( !outFile ) {
-            cerr << "Could not open " << m_settings->OutputFilename << " for output." << endl; 
+            cerr << "bamtools coverage ERROR: could not open " << m_settings->OutputFilename
+                 << " for output" << endl;
             return false; 
         }
         
@@ -123,7 +122,12 @@ bool CoverageTool::CoverageToolPrivate::Run(void) {
     
     //open our BAM reader
     BamReader reader;
-    reader.Open(m_settings->InputBamFilename);
+    if ( !reader.Open(m_settings->InputBamFilename) ) {
+        cerr << "bamtools coverage ERROR: could not open input BAM file: " << m_settings->InputBamFilename << endl;
+        return false;
+    }
+
+    // retrieve references
     m_references = reader.GetReferenceData();
     
     // set up our output 'visitor'
@@ -140,7 +144,8 @@ bool CoverageTool::CoverageToolPrivate::Run(void) {
     
     // clean up 
     reader.Close();
-    if ( m_settings->HasOutputFile ) outFile.close();
+    if ( m_settings->HasOutputFile )
+        outFile.close();
     delete cv;
     cv = 0;