added warning for duplicate @RG tag in header

[bamtools.git] / bamtools.cpp

diff --git a/bamtools.cpp b/bamtools.cpp
index 12731f21cbabeaf41107ae955a55e7921ed5ce2a..1dc16d1c0c1976a943ebb07a80bc9c9242b46ed3 100644 (file)
--- a/bamtools.cpp
+++ b/bamtools.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College
 // All rights reserved.
 // ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
+// Last modified: 2 June 2010
 // ---------------------------------------------------------------------------
 // Integrates a number of BamTools functionalities into a single executable.
 // ***************************************************************************
@@ -12,8 +12,10 @@
 #include <iostream>
 
 // BamTools includes
+#include "bamtools_convert.h"
 #include "bamtools_count.h"
 #include "bamtools_coverage.h"
+#include "bamtools_filter.h"
 #include "bamtools_header.h"
 #include "bamtools_index.h"
 #include "bamtools_merge.h"
@@ -26,8 +28,10 @@ using namespace BamTools;
 
 // ------------------------------------------
 // bamtools subtool names
+static const string CONVERT  = "convert";
 static const string COUNT    = "count";
 static const string COVERAGE = "coverage";
+static const string FILTER   = "filter";
 static const string HEADER   = "header";
 static const string INDEX    = "index";
 static const string MERGE    = "merge";
@@ -50,46 +54,50 @@ static const string SHORT_VERSION = "-v";
 int Help(int argc, char* argv[]) {
   
     // 'bamtools help COMMAND'
-    AbstractTool* tool(0);
     if (argc > 2) {
+        
+        AbstractTool* tool(0);
+        if ( argv[2] == CONVERT )  tool = new ConvertTool;
         if ( argv[2] == COUNT )    tool = new CountTool;
         if ( argv[2] == COVERAGE ) tool = new CoverageTool;
+        if ( argv[2] == FILTER )   tool = new FilterTool;
         if ( argv[2] == HEADER )   tool = new HeaderTool;
         if ( argv[2] == INDEX )    tool = new IndexTool;
         if ( argv[2] == MERGE )    tool = new MergeTool;
         if ( argv[2] == SAM )      tool = new SamTool;
         if ( argv[2] == SORT )     tool = new SortTool;
         if ( argv[2] == STATS )    tool = new StatsTool;
+        
+        // if tool known, print its help screen
+        if ( tool ) return tool->Help();
     }
-    
-    if ( tool ) return tool->Help();
-    else {
-     
-        // either 'bamtools help' or unrecognized argument after 'help'
-        cerr << endl;
-        cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
-        cerr << endl;
-        cerr << "Available bamtools commands:" << endl;
-        cerr << "\tcount     Prints number of alignments in BAM file" << endl;
-        cerr << "\tcoverage  Prints coverage statistics from the input BAM file" << endl;
-        cerr << "\theader    Prints BAM header information" << endl;
-        cerr << "\tindex     Generates index for BAM file" << endl;
-        cerr << "\tmerge     Merge multiple BAM files into single file" << endl;
-        cerr << "\tsam       Prints the BAM file in SAM (text) format" << endl;
-        cerr << "\tsort      Sorts the BAM file according to some criteria" << endl;
-        cerr << "\tstats     Prints some basic statistics from the input BAM file" << endl;
-        cerr << endl;
-        cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
-        cerr << endl;
-        return 0;
-    }
+
+    // either 'bamtools help' or unrecognized argument after 'help'
+    cerr << endl;
+    cerr << "usage: bamtools [--help] COMMAND [ARGS]" << endl;
+    cerr << endl;
+    cerr << "Available bamtools commands:" << endl;
+    cerr << "\tconvert   Converts between BAM and a number of other formats" << endl;
+    cerr << "\tcount     Prints number of alignments in BAM file" << endl;
+    cerr << "\tcoverage  Prints coverage statistics from the input BAM file" << endl;
+    cerr << "\tfilter    Filters BAM file(s) by user-specified criteria" << endl;
+    cerr << "\theader    Prints BAM header information" << endl;
+    cerr << "\tindex     Generates index for BAM file" << endl;
+    cerr << "\tmerge     Merge multiple BAM files into single file" << endl;
+    cerr << "\tsam       Prints the BAM file in SAM (text) format" << endl;
+    cerr << "\tsort      Sorts the BAM file according to some criteria" << endl;
+    cerr << "\tstats     Prints some basic statistics from the input BAM file" << endl;
+    cerr << endl;
+    cerr << "See 'bamtools help COMMAND' for more information on a specific command." << endl;
+    cerr << endl;
+    return 0;
 }
 
 // ------------------------------------------
 // Print version info
 int Version(void) {
     cout << endl;
-    cout << "bamtools v0.x.xx" << endl;
+    cout << "bamtools v0.8.xx" << endl;
     cout << "Part of BamTools API and toolkit" << endl;
     cout << "Primary authors: Derek Barnett, Erik Garrison, Michael Stromberg" << endl;
     cout << "(c) 2009-2010 Marth Lab, Biology Dept., Boston College" << endl;
@@ -112,8 +120,10 @@ int main(int argc, char* argv[]) {
         
     // determine desired sub-tool
     AbstractTool* tool(0);
+    if ( argv[1] == CONVERT )  tool = new ConvertTool;
     if ( argv[1] == COUNT )    tool = new CountTool;
     if ( argv[1] == COVERAGE ) tool = new CoverageTool;
+    if ( argv[1] == FILTER )   tool = new FilterTool;
     if ( argv[1] == HEADER )   tool = new HeaderTool;
     if ( argv[1] == INDEX )    tool = new IndexTool;
     if ( argv[1] == MERGE )    tool = new MergeTool;