Reorganized source tree & build system

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

diff --git a/src/toolkit/bamtools_filter.cpp b/src/toolkit/bamtools_filter.cpp
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+++ b/src/toolkit/bamtools_filter.cpp
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+// ***************************************************************************
+// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 1 June 2010
+// ---------------------------------------------------------------------------
+// Filters a single BAM file (or filters multiple BAM files and merges) 
+// according to some user-specified criteria.
+// ***************************************************************************
+
+#include <iostream>
+#include <string>
+#include <vector>
+
+#include "bamtools_filter.h"
+#include "bamtools_options.h"
+#include "BamReader.h"
+#include "BamMultiReader.h"
+
+using namespace std;
+using namespace BamTools; 
+  
+// ---------------------------------------------
+// FilterSettings implementation
+
+struct FilterTool::FilterSettings {
+
+    // flags
+    bool HasInputBamFilename;
+    bool HasOutputBamFilename;
+
+    // filenames
+    vector<string> InputFiles;
+    string OutputFilename;
+    
+    // constructor
+    FilterSettings(void)
+        : HasInputBamFilename(false)
+        , HasOutputBamFilename(false)
+        , OutputFilename(Options::StandardOut())
+    { }
+};  
+
+// ---------------------------------------------
+// FilterTool implementation
+
+FilterTool::FilterTool(void)
+    : AbstractTool()
+    , m_settings(new FilterSettings)
+{
+    // set program details
+    Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", "-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::StandardIn());
+    Options::AddValueOption("-out", "BAM filename", "the output BAM file",   "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+}
+
+FilterTool::~FilterTool(void) {
+    delete m_settings;
+    m_settings = 0;
+}
+
+int FilterTool::Help(void) {
+    Options::DisplayHelp();
+    return 0;
+}
+
+int FilterTool::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());
+    
+    // open files
+    BamMultiReader reader;
+    reader.Open(m_settings->InputFiles, false);
+        
+    // do filtering
+    
+    // clean up & exit
+    reader.Close();
+    return 0;
+}
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