"Includes code under the following licenses" note added.

LICENSE

@@ -29,4 +29,122 @@ d) make other distribution arrangements with the Copyright Holder.
 8. Aggregation of this Package with a commercial distribution is always permitted provided that the use of this Package is embedded; that is, when no overt attempt is made to make this Package's interfaces visible to the end user of the commercial distribution. Such use shall not be construed as a distribution of this Package.
 9. The name of the Copyright Holder may not be used to endorse or promote products derived from this software without specific prior written permission.
 10. THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
-The End
+The End
+
+
+Includes code under the following licenses:
+
+Templatized C++ Command Line Parser Library
+http://tclap.sourceforge.net/
+
+/******************************************************************************
+ *
+ *  Copyright (c) 2003, Michael E. Smoot .
+ *  Copyright (c) 2004, Michael E. Smoot, Daniel Aarno .
+ *  All rights reverved.
+ *
+ *  See the file COPYING in the top directory of this distribution for
+ *  more information.
+ *
+ *  THE SOFTWARE IS PROVIDED _AS IS_, WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ *  OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ *  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+ *  THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ *  FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ *  DEALINGS IN THE SOFTWARE.
+ *
+ *****************************************************************************/
+
+
+bamtools
+https://github.com/pezmaster31/bamtools
+
+The MIT License
+
+Copyright (c) 2009-2010 Derek Barnett, Erik Garrison, Gabor Marth, Michael Stromberg
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
+
+
+A Massively Spiffy Yet Delicately Unobtrusive Compression Library (zlib)
+http://www.zlib.net/
+
+Copyright notice:
+
+ (C) 1995-2012 Jean-loup Gailly and Mark Adler
+
+  This software is provided 'as-is', without any express or implied
+  warranty.  In no event will the authors be held liable for any damages
+  arising from the use of this software.
+
+  Permission is granted to anyone to use this software for any purpose,
+  including commercial applications, and to alter it and redistribute it
+  freely, subject to the following restrictions:
+
+  1. The origin of this software must not be misrepresented; you must not
+     claim that you wrote the original software. If you use this software
+     in a product, an acknowledgment in the product documentation would be
+     appreciated but is not required.
+  2. Altered source versions must be plainly marked as such, and must not be
+     misrepresented as being the original software.
+  3. This notice may not be removed or altered from any source distribution.
+
+  Jean-loup Gailly        Mark Adler
+  jloup@gzip.org          madler@alumni.caltech.edu
+
+If you use the zlib library in a product, we would appreciate *not* receiving
+lengthy legal documents to sign.  The sources are provided for free but without
+warranty of any kind.  The library has been entirely written by Jean-loup
+Gailly and Mark Adler; it does not include third-party code.
+
+If you redistribute modified sources, we would appreciate that you include in
+the file ChangeLog history information documenting your changes.  Please read
+the FAQ for more information on the distribution of modified source versions.
+
+
+FASTA/FASTQ Parser in C
+http://lh3lh3.users.sourceforge.net/parsefastq.shtml
+
+/* Contact: Heng Li <lh3@sanger.ac.uk> */
+
+/* The MIT License
+
+   Copyright (c) 2008 Genome Research Ltd (GRL).
+
+   Permission is hereby granted, free of charge, to any person obtaining
+   a copy of this software and associated documentation files (the
+   "Software"), to deal in the Software without restriction, including
+   without limitation the rights to use, copy, modify, merge, publish,
+   distribute, sublicense, and/or sell copies of the Software, and to
+   permit persons to whom the Software is furnished to do so, subject to
+   the following conditions:
+
+   The above copyright notice and this permission notice shall be
+   included in all copies or substantial portions of the Software.
+
+   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+   SOFTWARE.
+*/