From: Derek <derekwbarnett@gmail.com>
Date: Wed, 26 May 2010 20:16:03 +0000 (-0400)
Subject: Removed BamConversionMain.cpp and BamDumpMain.cpp. No longer needed if toolkit available.
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=cebdcc01b264653dc17227b6b2391645661e978a;p=bamtools.git

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

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