Marth Lab
Biology Dept., Boston College
-Email: barnetde@bc.edu
-Project Websites: http://github.com/pezmaster31/bamtools (ACTIVE SUPPORT)
- http://sourceforge.net/projects/bamtools (major updates only)
+Email: derekwbarnett@gmail.com
+Project Website: http://github.com/pezmaster31/bamtools
// ***************************************************************************
// BamAlignment.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 22 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamAlignment.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 22 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************\r
// BamAux.h (c) 2009 Derek Barnett, Michael Str�mberg\r
// Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
// ---------------------------------------------------------------------------\r
// Last modified: 4 March 2011 (DB)\r
// ---------------------------------------------------------------------------\r
// ***************************************************************************
// BamConstants.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamIndex.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 5 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamMultiReader.cpp (c) 2010 Erik Garrison, Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 15 March 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 15 March 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 4 March 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************\r
// BamReader.h (c) 2009 Derek Barnett, Michael Str�mberg\r
// Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
// ---------------------------------------------------------------------------\r
// Last modified: 4 March 2011 (DB)\r
// ---------------------------------------------------------------------------\r
// ***************************************************************************\r
// BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett\r
// Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
// ---------------------------------------------------------------------------\r
// Last modified: 4 March 2011 (DB)\r
// ---------------------------------------------------------------------------\r
// ***************************************************************************\r
// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett\r
// Marth Lab, Department of Biology, Boston College\r
-// All rights reserved.\r
// ---------------------------------------------------------------------------\r
// Last modified: 4 March 2011 (DB)\r
// ---------------------------------------------------------------------------\r
// ***************************************************************************
// SamConstants.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamHeader.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamHeader.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamProgram.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamProgram.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamProgramChain.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamProgramChain.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamReadGroup.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamReadGroup.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamReadGroupDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamReadGroupDictionary.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamSequence.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamSequence.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamSequenceDictionary.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamSequenceDictionary.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// api_global.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamHeader_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 21 March 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamHeader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 26 January 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamIndexFactory_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 5 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamIndexFactory_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 5 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamMultiMerger_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 9 September 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamMultiReader_p.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 9 September 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamMultiReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 9 September 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamRandomAccessController_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 5 April 2011(DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamRandomAccessController_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 24 February 2011(DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamReader_p.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 10 May 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 5 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamStandardIndex.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 24 June 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamStandardIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 24 June 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamToolsIndex.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 27 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamToolsIndex.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 5 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamWriter_p.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 16 June 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BamWriter_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 24 February 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BgzfStream_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 2 September 2011(DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// BgzfStream_p.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 5 April 2011(DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamFormatParser.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamFormatParser.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 23 December 2010 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamFormatPrinter.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamFormatPrinter.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 23 December 2010 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamHeaderValidator.cpp (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamHeaderValidator.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 13 January 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// SamHeaderVersion.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 24 February 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_global.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 3 March 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 May 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_convert.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 11 June 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_convert.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 9 July 2010
// ---------------------------------------------------------------------------
} // namespace BamTools
-#endif // BAMTOOLS_CONVERT_H
\ No newline at end of file
+#endif // BAMTOOLS_CONVERT_H
// ***************************************************************************
// bamtools_count.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_count.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_coverage.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_coverage.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 1 August 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_filter.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 28 August 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_header.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_index.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_index.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_merge.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_random.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_random.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2010 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_resolve.cpp (c) 2011
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 6 July 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_resolve.h (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 23 June 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_revert.cpp (c) 2010 Derek Barnett, Alistair Ward
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_revert.h (c) 2010 Derek Barnett, Alistair Ward
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_sort.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 14 June 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_sort.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_split.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_split.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_stats.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_tool.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 2 June 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_version.h.in (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010 (DB)
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_fasta.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 13 July 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_fasta.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_filter_engine.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_filter_properties.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_filter_ruleparser.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_options.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 11 June 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_options.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 11 June 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_pileup_engine.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_pileup_engine.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 18 September 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_utilities.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 9 June 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_utilities.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 9 June 2011
// ---------------------------------------------------------------------------
// ***************************************************************************
// bamtools_variant.h (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010
// ---------------------------------------------------------------------------
// ***************************************************************************
// utils_global.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
// Last modified: 19 November 2010 (DB)
// ---------------------------------------------------------------------------