Reorganized source tree & build system

[bamtools.git] / src / toolkit / bamtools_merge.cpp

diff --git a/src/toolkit/bamtools_merge.cpp b/src/toolkit/bamtools_merge.cpp
new file mode 100644 (file)
index 0000000..dcea172
--- /dev/null
+++ b/src/toolkit/bamtools_merge.cpp
@@ -0,0 +1,112 @@
+// ***************************************************************************
+// bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 2 June 2010
+// ---------------------------------------------------------------------------
+// Merges multiple BAM files into one.
+//
+// ** Provide selectable region? eg chr2:10000..20000
+//
+// ***************************************************************************
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "bamtools_merge.h"
+#include "bamtools_options.h"
+#include "bamtools_utilities.h"
+#include "BamMultiReader.h"
+#include "BamWriter.h"
+
+using namespace std;
+using namespace BamTools;
+
+// ---------------------------------------------
+// MergeSettings implementation
+
+struct MergeTool::MergeSettings {
+
+    // flags
+    bool HasInputBamFilename;
+    bool HasOutputBamFilename;
+//     bool HasRegion;
+    
+    // filenames
+    vector<string> InputFiles;
+    
+    // other parameters
+    string OutputFilename;
+//     string Region;
+    
+    // constructor
+    MergeSettings(void)
+        : HasInputBamFilename(false)
+        , HasOutputBamFilename(false)
+//         , HasRegion(false)
+        , OutputFilename(Options::StandardOut())
+    { }
+};  
+
+// ---------------------------------------------
+// MergeTool implementation
+
+MergeTool::MergeTool(void)
+    : AbstractTool()
+    , m_settings(new MergeSettings)
+{
+    // set program details
+    Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-out <filename>]");
+    
+    // set up options 
+    OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
+    Options::AddValueOption("-in",  "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename,  m_settings->InputFiles,     IO_Opts);
+    Options::AddValueOption("-out", "BAM filename", "the output BAM file",   "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
+    
+//     OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
+//     Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+}
+
+MergeTool::~MergeTool(void) {
+    delete m_settings;
+    m_settings = 0;
+}
+
+int MergeTool::Help(void) {
+    Options::DisplayHelp();
+    return 0;
+}
+
+int MergeTool::Run(int argc, char* argv[]) {
+  
+    // parse command line arguments
+    Options::Parse(argc, argv, 1);
+    
+     // set to default input if none provided
+    if ( !m_settings->HasInputBamFilename ) m_settings->InputFiles.push_back(Options::StandardIn());
+    
+    // opens the BAM files without checking for indexes
+    BamMultiReader reader;
+    reader.Open(m_settings->InputFiles, false, true); 
+
+    // retrieve header & reference dictionary info
+    std::string mergedHeader = reader.GetHeaderText();
+    RefVector references = reader.GetReferenceData();
+
+    // open BamWriter
+    BamWriter writer;
+    writer.Open(m_settings->OutputFilename, mergedHeader, references);
+
+    // store alignments to output file
+    BamAlignment bAlignment;
+    while (reader.GetNextAlignmentCore(bAlignment)) {
+        writer.SaveAlignment(bAlignment);
+    }
+    
+    // clean & exit
+    reader.Close();
+    writer.Close();
+    return 0;  
+}