From: barnett <barnett@9efb377e-2e27-44b9-b91a-ec4abb80ed8b>
Date: Thu, 16 Jul 2009 15:02:14 +0000 (+0000)
Subject: Added BamConversion back to BamTools
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=9f6d489fc810c243df6d893d78c95ea113da489d;p=bamtools.git

Added BamConversion back to BamTools
Updated Makefile

git-svn-id: svn+ssh://gene.bc.edu/home/subversion/Derek/BamTools/trunk@22 9efb377e-2e27-44b9-b91a-ec4abb80ed8b
---

diff --git a/BamConversionMain.cpp b/BamConversionMain.cpp
new file mode 100644
index 0000000..51693b6
--- /dev/null
+++ b/BamConversionMain.cpp
@@ -0,0 +1,41 @@
+#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/Makefile b/Makefile
index a056ae5..b2b6c92 100644
--- a/Makefile
+++ b/Makefile
@@ -1,10 +1,13 @@
 CXX=		g++
 CXXFLAGS=	-Wall -O3
-PROG=		BamDump BamTrim
+PROG=		BamConversion BamDump BamTrim
 LIBS=		-lz
 
 all: $(PROG)
 
+BamConversion: BamReader.o BamWriter.o BamConversionMain.o
+	$(CXX) $(CXXFLAGS) -o $@ BamReader.o BamWriter.o BamConversionMain.o $(LIBS)
+
 BamDump: BamReader.o BamDumpMain.o
 	$(CXX) $(CXXFLAGS) -o $@ BamReader.o BamDumpMain.o $(LIBS)