Brought API up to compliance with recent SAM Format Spec (v1.4-r962)

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

diff --git a/src/toolkit/bamtools_resolve.cpp b/src/toolkit/bamtools_resolve.cpp
new file mode 100644 (file)
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+++ b/src/toolkit/bamtools_resolve.cpp
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+// ***************************************************************************
+// bamtools_resolve.cpp (c) 2011
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 7 April 2011
+// ---------------------------------------------------------------------------
+// Resolves paired-end reads (marking the IsProperPair flag as needed)
+// ***************************************************************************
+
+#include "bamtools_resolve.h"
+
+#include <api/BamReader.h>
+#include <api/BamWriter.h>
+#include <utils/bamtools_options.h>
+#include <utils/bamtools_utilities.h>
+using namespace BamTools;
+
+#include <iostream>
+#include <string>
+using namespace std;
+
+// ---------------------------------------------
+// ResolveSettings implementation
+
+struct ResolveTool::ResolveSettings {
+
+    // flags
+    bool HasInput;
+    bool HasOutput;
+    bool IsForceCompression;
+
+    // filenames
+    string InputFilename;
+    string OutputFilename;
+
+    // constructor
+    ResolveSettings(void)
+        : HasInput(false)
+        , HasOutput(false)
+        , IsForceCompression(false)
+        , InputFilename(Options::StandardIn())
+        , OutputFilename(Options::StandardOut())
+    { }
+};
+
+// ---------------------------------------------
+// ResolveToolPrivate implementation
+
+struct ResolveTool::ResolveToolPrivate {
+
+    // ctor & dtor
+    public:
+        ResolveToolPrivate(ResolveTool::ResolveSettings* settings)
+            : m_settings(settings)
+        { }
+
+        ~ResolveToolPrivate(void) { }
+
+    // 'public' interface
+    public:
+        bool Run(void);
+
+    // internal methods
+    private:
+
+    // data members
+    private:
+        ResolveTool::ResolveSettings* m_settings;
+};
+
+bool ResolveTool::ResolveToolPrivate::Run(void) {
+    cerr << "Resoling BAM file..." << endl;
+    return true;
+}
+
+// ---------------------------------------------
+// ResolveTool implementation
+
+ResolveTool::ResolveTool(void)
+    : AbstractTool()
+    , m_settings(new ResolveSettings)
+    , m_impl(0)
+{
+    // set program details
+    Options::SetProgramInfo("bamtools resolve", "resolves paired-end reads (marking the IsProperPair flag as needed)", "[-in <filename> -in <filename> ...] [-out <filename> | [-forceCompression]] [resolveOptions]");
+
+    // set up options
+    OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
+    Options::AddValueOption("-in",  "BAM filename", "the input BAM file",  "", m_settings->HasInput,  m_settings->InputFilename,  IO_Opts, Options::StandardIn());
+    Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+    Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
+}
+
+ResolveTool::~ResolveTool(void) {
+
+    delete m_settings;
+    m_settings = 0;
+
+    delete m_impl;
+    m_impl = 0;
+}
+
+int ResolveTool::Help(void) {
+    Options::DisplayHelp();
+    return 0;
+}
+
+int ResolveTool::Run(int argc, char* argv[]) {
+
+    // parse command line arguments
+    Options::Parse(argc, argv, 1);
+
+    // initialize ResolveTool
+    m_impl = new ResolveToolPrivate(m_settings);
+
+    // run ResolveTool, return success/failure
+    if ( m_impl->Run() ) return 0;
+    else return 1;
+}