merge master 2.3.0

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

diff --git a/src/toolkit/bamtools_header.cpp b/src/toolkit/bamtools_header.cpp
index aad413f29df916ec0edade03eac4206770e0bac2..534bb14e1cbbe03716fdb8856e32c31db340bdcc 100644 (file)
--- a/src/toolkit/bamtools_header.cpp
+++ b/src/toolkit/bamtools_header.cpp
@@ -1,9 +1,8 @@
 // ***************************************************************************
 // bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison
 // Marth Lab, Department of Biology, Boston College
-// All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 21 March 2011
+// Last modified: 10 December 2012
 // ---------------------------------------------------------------------------
 // Prints the SAM-style header from a single BAM file ( or merged header from
 // multiple BAM files) to stdout
@@ -15,6 +14,7 @@
 #include <utils/bamtools_options.h>
 using namespace BamTools;
 
+#include <fstream>
 #include <iostream>
 #include <string>
 #include <vector>
@@ -26,35 +26,98 @@ using namespace std;
 struct HeaderTool::HeaderSettings {
 
     // flags
-    bool HasInputBamFilename;
+    bool HasInput;
+    bool HasInputFilelist;
 
     // filenames
     vector<string> InputFiles;
+    string InputFilelist;
     
     // constructor
     HeaderSettings(void)
-        : HasInputBamFilename(false)
+        : HasInput(false)
+        , HasInputFilelist(false)
     { }
 };  
 
+struct HeaderTool::HeaderToolPrivate {
+
+    // ctor & dtor
+    public:
+        HeaderToolPrivate(HeaderTool::HeaderSettings* settings)
+            : m_settings(settings)
+        { }
+
+        ~HeaderToolPrivate(void) { }
+
+    // interface
+    public:
+        bool Run(void);
+
+    // data members
+    private:
+        HeaderTool::HeaderSettings* m_settings;
+};
+
+bool HeaderTool::HeaderToolPrivate::Run(void) {
+
+    // set to default input if none provided
+    if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
+        m_settings->InputFiles.push_back(Options::StandardIn());
+
+    // add files in the filelist to the input file list
+    if ( m_settings->HasInputFilelist ) {
+
+        ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+        if ( !filelist.is_open() ) {
+            cerr << "bamtools header ERROR: could not open input BAM file list... Aborting." << endl;
+            return false;
+        }
+
+        string line;
+        while ( getline(filelist, line) )
+            m_settings->InputFiles.push_back(line);
+    }
+
+    // attemp to open BAM files
+    BamMultiReader reader;
+    if ( !reader.Open(m_settings->InputFiles) ) {
+        cerr << "bamtools header ERROR: could not open BAM file(s) for reading... Aborting." << endl;
+        return false;
+    }
+
+    // dump (merged) header contents to stdout
+    cout << reader.GetHeaderText() << endl;
+
+    // clean up & exit
+    reader.Close();
+    return true;
+}
+
 // ---------------------------------------------
 // HeaderTool implementation
 
 HeaderTool::HeaderTool(void)
     : AbstractTool()
     , m_settings(new HeaderSettings)
+    , m_impl(0)
 {
     // set program details
-    Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "[-in <filename> -in <filename> ...] ");
+    Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "[-in <filename> -in <filename> ... | -list <filelist>]");
     
     // 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("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+    Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist,  m_settings->InputFilelist, IO_Opts);
 }
 
 HeaderTool::~HeaderTool(void) {
+
     delete m_settings;
     m_settings = 0;
+
+    delete m_impl;
+    m_impl = 0;
 }
 
 int HeaderTool::Help(void) {
@@ -67,21 +130,12 @@ int HeaderTool::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());
-    
-    // attemp to open BAM files
-    BamMultiReader reader;
-    if ( !reader.Open(m_settings->InputFiles) ) {
-        cerr << "bamtools header ERROR: could not open BAM file(s) for reading... Aborting." << endl;
-        return 1;
-    }
+    // initialize HeaderTool with settings
+    m_impl = new HeaderToolPrivate(m_settings);
 
-    // dump (merged) header contents to stdout
-    cout << reader.GetHeaderText() << endl;
-
-    // clean up & exit
-    reader.Close();
-    return 0;
+    // run HeaderTool, return success/fail
+    if ( m_impl->Run() )
+        return 0;
+    else
+        return 1;
 }