// ***************************************************************************
// bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 March 2011 (DB)
+// Last modified: 18 May 2011 (DB)
// ---------------------------------------------------------------------------
// Integrates a number of BamTools functionalities into a single executable.
// ***************************************************************************
#include "bamtools_index.h"
#include "bamtools_merge.h"
#include "bamtools_random.h"
+#include "bamtools_resolve.h"
#include "bamtools_revert.h"
#include "bamtools_sort.h"
#include "bamtools_split.h"
static const string INDEX = "index";
static const string MERGE = "merge";
static const string RANDOM = "random";
+static const string RESOLVE = "resolve";
static const string REVERT = "revert";
static const string SORT = "sort";
static const string SPLIT = "split";
if ( arg == INDEX ) return new IndexTool;
if ( arg == MERGE ) return new MergeTool;
if ( arg == RANDOM ) return new RandomTool;
+ if ( arg == RESOLVE ) return new ResolveTool;
if ( arg == REVERT ) return new RevertTool;
if ( arg == SORT ) return new SortTool;
if ( arg == SPLIT ) return new SplitTool;
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 << "\trandom Select random alignments from existing BAM file(s)" << endl;
+ cerr << "\trandom Select random alignments from existing BAM file(s), intended more as a testing tool." << endl;
+ cerr << "\tresolve Resolves paired-end reads (marking the IsProperPair flag as needed)" << endl;
cerr << "\trevert Removes duplicate marks and restores original base qualities" << endl;
cerr << "\tsort Sorts the BAM file according to some criteria" << endl;
cerr << "\tsplit Splits a BAM file on user-specified property, creating a new BAM output file for each value found" << endl;