json output

[bamtools.git] / bamtools_merge.h

diff --git a/bamtools_merge.h b/bamtools_merge.h
index 1f9be7086db690ac34eed1c5f727c118512d0642..2962ce82943b54a137299e9379d963485dde4e3c 100644 (file)
--- a/bamtools_merge.h
+++ b/bamtools_merge.h
@@ -3,93 +3,33 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 26 May 2010
+// Last modified: 1 June 2010
 // ---------------------------------------------------------------------------
-// Merges multiple BAM files into one.
-//
-// ** Provide selectable region? eg chr2:10000..20000
-//
+// Merges multiple BAM files into one
 // ***************************************************************************
 
 #ifndef BAMTOOLS_MERGE_H
 #define BAMTOOLS_MERGE_H
 
-#include <iostream>
-#include <string>
-#include <vector>
-
-#include "BamMultiReader.h"
-#include "BamWriter.h"
-// #include "GetOpt.h"
-#include "bamtools_getopt.h"
+#include "bamtools_tool.h"
 
 namespace BamTools {
-
-int BamMergeHelp(void) { 
-    std::cerr << std::endl;
-    std::cerr << "usage:\tbamtools merge [--out FILE] [--region REGION] [--in FILE [FILE] [FILE] ...] " << std::endl;
-    std::cerr << std::endl;
-    std::cerr << "\t--in FILE        Input BAM file(s)                      [stdin]" << std::endl;
-    std::cerr << "\t--region REGION  Only keep alignments from this region. [all alignments]" << std::endl;
-    std::cerr << "\t                 REGION format - (eg chr2:1000..2000)" << std::endl;
-    std::cerr << "\t--out FILE       Destination for merge results          [stdout]" << std::endl;
-    std::cerr << std::endl;
-    return 0;
-}
-
-int RunBamMerge(int argc, char* argv[]) {
   
-    // only 'bamtool merge', show help
-    if ( argc == 2 ) return BamMergeHelp();
+class MergeTool : public AbstractTool {
+  
+    public:
+        MergeTool(void);
+        ~MergeTool(void);
+  
+    public:
+        int Help(void);
+        int Run(int argc, char* argv[]); 
+        
+    private:
+        struct MergeSettings;
+        MergeSettings* m_settings;
+};
   
-    // else parse command line for args
-    GetOpt options(argc, argv, 1);
-    
-    std::string outputFilename = "";
-    options.addOption("out", &outputFilename);
-    
-    std::vector<std::string> inputFilenames;
-    options.addVariableLengthOption("in", &inputFilenames);
-    
-    std::string regionString;
-    options.addOption("region", &regionString);
-    
-    if ( !options.parse() || inputFilenames.empty() ) return BamMergeHelp();   
-    if ( inputFilenames.empty() ) { inputFilenames.push_back("stdin"); }
-    if ( outputFilename.empty() ) { outputFilename = "stdout"; }
-    
-    // opens the BAM files without checking for indexes
-    BamMultiReader reader;
-    reader.Open(inputFilenames, false); 
-
-    // retrieve header & reference dictionary info
-    std::string mergedHeader = reader.GetHeaderText();
-    RefVector references = reader.GetReferenceData();
-
-    // open BamWriter
-    BamWriter writer;
-    writer.Open(outputFilename, mergedHeader, references);
-
-    // if desired region provided
-    if ( !regionString.empty() ) {
-        // parse region string
-        // only get alignments from this region
-    } 
-    
-    // else get all alignments
-    else {
-        // store alignments to output file
-        BamAlignment bAlignment;
-        while (reader.GetNextAlignment(bAlignment)) {
-            writer.SaveAlignment(bAlignment);
-        }
-    }
-    // clean & exit
-    reader.Close();
-    writer.Close();
-    return 0;  
-}
-
 } // namespace BamTools
 
-#endif // BAMTOOLS_MERGE_H
\ No newline at end of file
+#endif // BAMTOOLS_MERGE_H