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Remove all licenses from the files and unify them in the LICENSE file
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Closes #13
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@ljyanesm
ljyanesm committed Aug 7, 2019
1 parent cc5b04b commit 5e08524
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2 changes: 1 addition & 1 deletion LICENSE
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Copyright (c) 2014 Broad Institute
Copyright (c) 2004-2016 Broad Institute
Copyright (c) 2016 The Genome Analysis Centre

Permission is hereby granted, free of charge, to any person obtaining a copy
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8 changes: 0 additions & 8 deletions src/Basevector.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

/*
* \file Basevector.cc
* \author tsharpe
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8 changes: 0 additions & 8 deletions src/Basevector.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef BASEVECTOR_H_
#define BASEVECTOR_H_

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9 changes: 0 additions & 9 deletions src/BasevectorTools.cc
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/////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2007) by the //
// Broad Institute/Massachusetts Institute of Technology. All rights //
// are reserved. This software is supplied without any warranty or //
// guaranteed support whatsoever. Neither the Broad Institute nor MIT //
// can be responsible for its use, misuse, or functionality. //
/////////////////////////////////////////////////////////////////////////////

#include "BasevectorTools.h"

9 changes: 0 additions & 9 deletions src/BasevectorTools.h
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/////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2007) by the //
// Broad Institute/Massachusetts Institute of Technology. All rights //
// are reserved. This software is supplied without any warranty or //
// guaranteed support whatsoever. Neither the Broad Institute nor MIT //
// can be responsible for its use, misuse, or functionality. //
/////////////////////////////////////////////////////////////////////////////

// File: BasevectorTools.h
//
// This file defines some handy and generic enough methods to be used with/
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8 changes: 0 additions & 8 deletions src/Bitvector.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef BITVECTOR_H_
#define BITVECTOR_H_

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8 changes: 0 additions & 8 deletions src/Block.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef BLOCK_H
#define BLOCK_H

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8 changes: 0 additions & 8 deletions src/Charvector.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

/*
* \file Charvector.cc
* \author tsharpe
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8 changes: 0 additions & 8 deletions src/Charvector.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

/*
* \file Charvector.h
* \author jbutler
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8 changes: 0 additions & 8 deletions src/CommonSemanticTypes.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

/**
Header: CommonSemanticTypes.h
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7 changes: 0 additions & 7 deletions src/Compare.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////
/*
* \file Compare.h
* \author tsharpe
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8 changes: 0 additions & 8 deletions src/CoreTools.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef CORE_TOOLS_H
#define CORE_TOOLS_H

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8 changes: 0 additions & 8 deletions src/Equiv.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#include "Equiv.h"
#include "Vec.h"

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8 changes: 0 additions & 8 deletions src/Equiv.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef EQUIV_H
#define EQUIV_H

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8 changes: 0 additions & 8 deletions src/FastIfstream.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#include <sys/types.h>

#include "CoreTools.h"
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8 changes: 0 additions & 8 deletions src/FastIfstream.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

// This file defines class fast_ifstream and fast_pipe_ifstream, which has
// essentially identical member functions.

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8 changes: 0 additions & 8 deletions src/Fastavector.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2015) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#include "Fastavector.h"
#include "Bitvector.h"
#include "graph/Digraph.h"
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8 changes: 0 additions & 8 deletions src/Fastavector.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

// This file defines "fastavector", which stores bases in fasta format.

#ifndef FASTA_VECTOR
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8 changes: 0 additions & 8 deletions src/FeudalMimic.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

// Mimic: given a vecbasevector, generate a vecbitbector which has the same
// "dimensions", so that there is a bijective correspondence between bases in one
// and bits in the other. (Also set the bitvector entries to False.) Other similar
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7 changes: 0 additions & 7 deletions src/IntPairVec.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2012) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////
/*
* \file IntPairVec.cc
* \author tsharpe
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2012) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////
/*
* \file IntPairVec.h
* \author tsharpe
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8 changes: 0 additions & 8 deletions src/Intvector.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

/*
* \file Intvector.cc
* \author tsharpe
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11 changes: 1 addition & 10 deletions src/Intvector.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////


// This file defines the typedef "intvector", which stores
// This file defines the typedef "intvector", which stores
// a vector of ints, and the typedef "vecintvector", which
// stores a vector of intvectors.

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7 changes: 0 additions & 7 deletions src/IteratorRange.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2012) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////
/*
* \file IteratorRange.h
* \author tsharpe
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8 changes: 0 additions & 8 deletions src/MainTools.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef MAIN_TOOLS_H
#define MAIN_TOOLS_H

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8 changes: 0 additions & 8 deletions src/Map.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef MAP_H
#define MAP_H

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7 changes: 0 additions & 7 deletions src/MapReduceEngine.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2015) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////
/*
* MapReduceEngine.h
*
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8 changes: 0 additions & 8 deletions src/MemberOf.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#include "dvString.h"
#include "Vec.h"
#include "ParseSet.h"
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8 changes: 0 additions & 8 deletions src/MemberOf.h
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////

#ifndef MEMBER_OF_H
#define MEMBER_OF_H

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9 changes: 0 additions & 9 deletions src/Misc.cc
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////


#include "Misc.h"

char PrintBool( Bool b ) {
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///////////////////////////////////////////////////////////////////////////////
// SOFTWARE COPYRIGHT NOTICE AGREEMENT //
// This software and its documentation are copyright (2010) by the //
// Broad Institute. All rights are reserved. This software is supplied //
// without any warranty or guaranteed support whatsoever. The Broad //
// Institute is not responsible for its use, misuse, or functionality. //
///////////////////////////////////////////////////////////////////////////////


#ifndef MISC
#define MISC

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