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Modified GPL boilerplate and added COPYING file to source tree.

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jts committed Feb 9, 2010
1 parent 44a6362 commit 821da1a62118ca2136c059afa2346a273b8d4916
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Bidirectional graph
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Base bidirectional edge class
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Vertex - Generic vertex class for bigraph
@@ -125,7 +125,7 @@ void Vertex::makeUnique()
m_edges.swap(uniqueVec);
}
-//
+// Ensure each edge of the vertex is unique
void Vertex::makeUnique(EdgeDir dir, EdgePtrVec& uniqueVec)
{
std::set<VertexID> idSet;
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// OverlapThread - Threaded implementation
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// assemble - convert read overlaps into contigs
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// extract - extract all sequences of a given length from a bwt
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// index - index reads using a suffix tree
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// overlap - compute pairwise overlaps between reads
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// oview - view overlap alignments
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// sga - Main assembler driver program
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// SGAlgorithms - Collection of algorithms for operating on string graphs
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// SGUtils - Data structures/Functions related
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// AssembleExact - Assembly algorithm for exact sequences using a BWT
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// BWT.cpp - Burrows Wheeler transform of a generalized suffix array
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// bwt_algorithms.cpp - Algorithms for aligning to a bwt structure
@@ -346,8 +346,10 @@ int BWTAlgorithms::alignSuffixExact(const std::string& w, const BWT* pBWT, const
// Calculate the ranges in pBWT that contain a prefix of at least minOverlap basepairs that
// overlaps with a suffix of w. The ranges are added to the pOBList
-void BWTAlgorithms::findOverlapBlocks(const std::string& w, const BWT* pBWT, const BWT* pRevBWT,
- int minOverlap, const AlignFlags& af, OverlapBlockList* pOBList, OverlapBlockList* pOBFinal)
+void BWTAlgorithms::findOverlapBlocks(const std::string& w, const BWT* pBWT,
+ const BWT* pRevBWT, int minOverlap,
+ const AlignFlags& af, OverlapBlockList* pOBList,
+ OverlapBlockList* pOBFinal)
{
// All overlaps are added to this list and then sub-maximal overlaps are removed
OverlapBlockList workingList;
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// BWTTraverse - traverse a bwt, outputting all
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// InverseSuffixArray - The inverse of a generalized suffix array
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// LCPArray - Longest Common Prefix array for a suffix array
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Occurrence.cpp - Data structure holding the number of times
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// OverlapBlock - Data structures holding
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// OverlapQuality - Probabilitic inference of the quality of a set of overlaps
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// STCommon.cpp - Implementation of basic data structures
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// SuffixArray - Generalized suffix array
@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// SuffixCompareRadix
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// saca - suffix array construction algorithms
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2010 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// BitChar - Fixed-size bitset of 8 bits
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// DNAString
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Interval - A pair of integers denoting a range
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Match - A pair of coordinates representing the overlapping
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Pileup - An array of strings containing all the seen
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// ReadTable - A 0-indexed table of reads
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// SeqCoord - A data structure holding the coordinate
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// SeqReader - Reads fasta or fastq sequence files
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// Util - Common data structures and functions
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@@ -1,7 +1,7 @@
//-----------------------------------------------
// Copyright 2009 Wellcome Trust Sanger Institute
// Written by Jared Simpson (js18@sanger.ac.uk)
-// Released under the GPL license
+// Released under the GPL
//-----------------------------------------------
//
// bucketSort - perform a bucket sort over a range of values

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