Removed BamConversionMain.cpp and BamDumpMain.cpp. No longer needed if toolkit available.

diff --git a/BamConversionMain.cpp b/BamConversionMain.cpp
deleted file mode 100644 (file)
index 51693b6..0000000
--- a/BamConversionMain.cpp
+++ /dev/null
@@ -1,41 +0,0 @@
-#include <iostream>
-#include "BamReader.h"
-#include "BamWriter.h"
-using namespace BamTools;
-using namespace std;
-
-int main(int argc, char* argv[]) {
-
-       if(argc != 3) {
-               cout << "USAGE: " << argv[0] << " <input BAM file> <output BAM file>" << endl;
-               exit(1);
-       }
-
-       // localize our arguments
-       const char* inputFilename  = argv[1];
-       const char* outputFilename = argv[2];
-
-       // open our BAM reader
-       BamReader reader;
-       reader.Open(inputFilename);
-
-       // retrieve the SAM header text
-       string samHeader = reader.GetHeaderText();
-
-       // retrieve the reference sequence vector
-       RefVector referenceSequences = reader.GetReferenceData();
-
-       // open the BAM writer
-       BamWriter writer;
-       writer.Open(outputFilename, samHeader, referenceSequences);
-
-       // copy all of the reads from the input file to the output file
-       BamAlignment al;
-       while(reader.GetNextAlignment(al)) writer.SaveAlignment(al);
-
-       // close our files
-       reader.Close();
-       writer.Close();
-
-       return 0;
-}

diff --git a/BamDumpMain.cpp b/BamDumpMain.cpp
deleted file mode 100644 (file)
index 5611c3b..0000000
--- a/BamDumpMain.cpp
+++ /dev/null
@@ -1,57 +0,0 @@
-// ***************************************************************************\r
-// BamDump.cpp (c) 2009 Derek Barnett\r
-// Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
-// ---------------------------------------------------------------------------\r
-// Last modified: 15 July 2009 (DB)\r
-// ---------------------------------------------------------------------------\r
-// Spits out all alignments in BAM file.\r
-//\r
-// N.B. - Could result in HUGE text file. This is mostly a debugging tool\r
-// for small files.  You have been warned.\r
-// ***************************************************************************\r
-\r
-// Std C/C++ includes\r
-#include <cstdlib>\r
-#include <iostream>\r
-#include <string>\r
-using namespace std;\r
-\r
-// BamTools includes\r
-#include "BamReader.h"\r
-#include "BamWriter.h"\r
-using namespace BamTools;\r
-\r
-void PrintAlignment(const BamAlignment&);\r
-\r
-int main(int argc, char* argv[]) {\r
-\r
-       // validate argument count\r
-       if( argc != 2 ) {\r
-               cerr << "USAGE: " << argv[0] << " <input BAM file> " << endl;\r
-               exit(1);\r
-       }\r
-\r
-       string filename = argv[1];\r
-       cout << "Printing alignments from file: " << filename << endl;\r
-       \r
-       BamReader reader;\r
-       reader.Open(filename);\r
-       \r
-       BamAlignment bAlignment;\r
-       while (reader.GetNextAlignment(bAlignment)) {\r
-            PrintAlignment(bAlignment);\r
-       }\r
-\r
-       reader.Close();\r
-       return 0;\r
-}\r
-       \r
-// Spit out basic BamAlignment data \r
-void PrintAlignment(const BamAlignment& alignment) {\r
-       cout << "---------------------------------" << endl;\r
-       cout << "Name: "       << alignment.Name << endl;\r
-       cout << "Aligned to: " << alignment.RefID;\r
-       cout << ":"            << alignment.Position << endl;\r
-        cout << endl;\r
-}\r