From 77f7ccd20d2a255f5f2f4200b458500144551ad6 Mon Sep 17 00:00:00 2001
From: Erik Garrison <erik.garrison@bc.edu>
Date: Fri, 21 May 2010 16:53:26 -0400
Subject: [PATCH] bamtools executable

Merge a number of useful tools into a single executable.

Also in this commit, addition of verification that reference sequences
are identical among readers opened by the BamMultiReader.  Without this
check the behavior of the MultiReader is undefined.
---
 bamtools.cpp | 126 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 126 insertions(+)
 create mode 100644 bamtools.cpp

diff --git a/bamtools.cpp b/bamtools.cpp
new file mode 100644
index 0000000..e4d7769
--- /dev/null
+++ b/bamtools.cpp
@@ -0,0 +1,126 @@
+// ***************************************************************************
+// bamtools.cpp (c) 2010 Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Integrates a number of BamTools functionalities into a single executable.
+// ***************************************************************************
+
+// Std C/C++ includes
+#include <cstdlib>
+#include <iostream>
+#include <string>
+#include <boost/algorithm/string.hpp>
+using namespace std;
+
+// BamTools includes
+#include "BamReader.h"
+#include "BamWriter.h"
+#include "BamMultiReader.h"
+using namespace BamTools;
+
+void usageSummary() {
+    cerr << "usage: bamtools <command> [options]" << endl
+         << "actions:" << endl
+         << "    index <bam file>" << endl
+         << "    merge <merged BAM file> [<BAM file> <BAM file> ...]" << endl
+         << "    dump [<BAM file> <BAM file> ...]" << endl;
+         //<< "    trim <input BAM file> <input BAM index file> <output BAM file> <reference name> <leftBound> <rightBound>" << endl;
+}
+
+
+void BamMerge(string outputFilename, vector<string> filenames) {
+
+    BamMultiReader reader;
+
+    reader.Open(filenames);
+
+    string mergedHeader = reader.GetHeaderText();
+
+    RefVector references = reader.GetReferenceData();
+
+    // open BamWriter
+    BamWriter writer;
+    writer.Open( outputFilename.c_str(), mergedHeader, references);
+
+    BamAlignment bAlignment;
+    while (reader.GetNextAlignment(bAlignment)) {
+        // write to output file
+        writer.SaveAlignment(bAlignment);
+    }
+
+    // close output file
+    writer.Close();
+    // close input files
+    reader.Close();
+
+}
+
+void BamCreateIndex(const char* inputFilename) {
+
+	// open our BAM reader
+	BamReader reader;
+	reader.Open(inputFilename);
+
+    // create index file
+    reader.CreateIndex();
+
+	// close our file
+	reader.Close();
+
+}
+
+// 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;
+}
+
+void BamDump(vector<string> files) {
+
+	BamMultiReader reader;
+	reader.Open(files);
+	
+	BamAlignment bAlignment;
+	while (reader.GetNextAlignment(bAlignment)) {
+            PrintAlignment(bAlignment);
+	}
+
+	reader.Close();
+
+}
+
+
+int main(int argc, char* argv[]) {
+
+	// validate argument count
+	if( argc < 2 ) {
+        usageSummary();
+		exit(1);
+	}
+
+    string command = argv[1];
+    
+    if (command == "index") {
+        BamCreateIndex(argv[2]);
+    } else if (command == "merge") {
+        vector<string> files;
+        string outputFile = argv[2];
+        for (int i = 3; i<argc; ++i) {
+            files.push_back(argv[i]);
+        }
+        BamMerge(outputFile, files);
+    } else if (command == "dump") {
+        vector<string> files;
+        for (int i = 2; i<argc; ++i) {
+            files.push_back(argv[i]);
+        }
+        BamDump(files);
+    }
+
+
+	return 0;
+}
-- 
2.39.2