license updates and help proofreading

marbl · Oct 22, 2015 · 989c955 · 989c955
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diff --git a/LICENSE.txt b/LICENSE.txt
@@ -3,15 +3,25 @@ PURPOSE
 Mash is a fast sequence distance estimator that uses the MinHash
 algorithm and is designed to work with genomes and metagenomes in the
 form of assemblies or reads. It is implemented in C++ and is
-distributed with KSeq (lh3lh3.users.sourceforge.net/kseq.shtml) and
-MurmurHash3 (code.google.com/p/smhasher/wiki/MurmurHash3).
+distributed with:
 
+KSeq
+  lh3lh3.users.sourceforge.net/kseq.shtml
+  MIT License
+
+MurmurHash3
+  code.google.com/p/smhasher/wiki/MurmurHash3
+  Public domain
+
+Open Bloom Filter
+  https://code.google.com/p/bloom/source/browse/trunk/bloom_filter.hpp
+  Common Public License
 
 COPYRIGHT LICENSE
 
 Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-Adam Phillippy
+all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+Sergey Koren, and Adam Phillippy
 
 This Software was prepared for the Department of Homeland Security
 (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as

diff --git a/src/mash/Command.cpp b/src/mash/Command.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 
@@ -162,7 +162,7 @@ Command::Command()
     addAvailableOption("individual", Option(Option::Boolean, "i", "Sketch", "Sketch individual sequences, rather than whole files.", ""));
     addAvailableOption("warning", Option(Option::Number, "w", "Sketch", "Probability threshold for warning about low k-mer size.", "0.01", 0, 1));
     addAvailableOption("unique", Option(Option::Boolean, "u", "Sketch", "Remove (most) unique kmers using a Bloom Filter. This is useful for reducing noise from sequencing errors in read sets. See Bloom filter options below. Incompatible with -i.", ""));
-    addAvailableOption("genome", Option(Option::Size, "g", "Bloom", "Expected genome size (raw bases, or with K/M/G/T). Helps pick the Bloom Filter size. Should be within an order of magnitude of the true size. Implies -u.", "5M"));
+    addAvailableOption("genome", Option(Option::Size, "g", "Bloom", "Expected genome size (raw bases or with K/M/G/T). Helps pick the Bloom Filter size. Should be within an order of magnitude of the true size. Implies -u.", "5M"));
     addAvailableOption("memory", Option(Option::Size, "m", "Bloom", "Maximum Bloom Filter memory usage (raw bytes or with K/M/G/T). More memory will allow more thorough detection of unique kmers, so this should be as high as is practical for the computing environment (though it may not actually be used). Implies -u.", "1G"));
     addAvailableOption("bloomError", Option(Option::Number, "e", "Bloom", "Target false-negative rate for Bloom filtering unique kmers with. Implies -u.", "0.1", 0, 1));
     addAvailableOption("noncanonical", Option(Option::Boolean, "n", "Sketch", "Non-canonical. By default, canonical DNA kmers (alphabetical minima of forward-reverse pairs) are used, and kmers with non-acgtACGT characters are ignored. This option uses kmers as they appear and allows all characters.", ""));

diff --git a/src/mash/Command.h b/src/mash/Command.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandContain.cpp b/src/mash/CommandContain.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandContain.h b/src/mash/CommandContain.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandDistance.cpp b/src/mash/CommandDistance.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 
@@ -25,7 +25,7 @@ CommandDistance::CommandDistance()
 {
     name = "dist";
     summary = "Estimate the distance of query sequences to references.";
-    description = "Estimate the distance of each query sequence to the reference. Both the reference and queries can be fasta or fastq, gzipped or not, or mash sketch files (.msh) with matching k-mer sizes. Query files can also be files of file names (see -l). Whole files are compared by default (see -i). The output fields are [reference-ID, query-ID, distance, p-value, shared-hashes].";
+    description = "Estimate the distance of each query sequence to the reference. Both the reference and queries can be fasta or fastq, gzipped or not, or Mash sketch files (.msh) with matching k-mer sizes. Query files can also be files of file names (see -l). Whole files are compared by default (see -i). The output fields are [reference-ID, query-ID, distance, p-value, shared-hashes].";
     argumentString = "<reference> <query> [<query>] ...";
 
     useOption("help");

diff --git a/src/mash/CommandDistance.h b/src/mash/CommandDistance.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandFind.cpp b/src/mash/CommandFind.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandFind.h b/src/mash/CommandFind.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandInfo.cpp b/src/mash/CommandInfo.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandInfo.h b/src/mash/CommandInfo.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandList.cpp b/src/mash/CommandList.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 
@@ -36,12 +36,7 @@ void CommandList::print()
 
     cout << endl << "Mash version " << version << endl << endl;
 
-    cout << "Copyright © 2015, Battelle National Biodefense Institute (BNBI); all rights" << endl;
-	cout << "reserved. Authored by: Brian Ondov, Todd Treangen, and Adam Phillippy." << endl;
-
-    cout << "This program is free software and comes with ABSOLUTELY NO WARRANTY, though you" << endl;
-    cout << "are welcome to redistribute it under certain conditions. Source code is" << endl;
-    cout << "available at github.com/marbl/mash. For more details, type 'mash --license'." << endl;
+    cout << "Type 'mash --license' for license and copyright information." << endl;
 
     cout << endl << "Usage:" << endl << endl;
 
@@ -103,8 +98,19 @@ PURPOSE\n\
 Mash is a fast sequence distance estimator that uses the MinHash\n\
 algorithm and is designed to work with genomes and metagenomes in the\n\
 form of assemblies or reads. It is implemented in C++ and is\n\
-distributed with KSeq (lh3lh3.users.sourceforge.net/kseq.shtml) and\n\
-MurmurHash3 (code.google.com/p/smhasher/wiki/MurmurHash3).\n\
+distributed with:\n\
+\n\
+KSeq\n\
+  lh3lh3.users.sourceforge.net/kseq.shtml\n\
+  MIT License\n\
+\n\
+MurmurHash3\n\
+  code.google.com/p/smhasher/wiki/MurmurHash3\n\
+  Public domain\n\
+\n\
+Open Bloom Filter\n\
+  https://code.google.com/p/bloom/source/browse/trunk/bloom_filter.hpp\n\
+  Common Public License\n\
 \n";
 #ifdef DIST_LICENSE
 	cout << "\n\
@@ -118,8 +124,8 @@ cout << "\n\
 COPYRIGHT LICENSE\n\
 \n\
 Copyright © 2015, Battelle National Biodefense Institute (BNBI);\n\
-all rights reserved. Authored by: Brian Ondov, Todd Treangen, and\n\
-Adam Phillippy\n\
+all rights reserved. Authored by: Brian Ondov, Todd Treangen,\n\
+Sergey Koren, and Adam Phillippy\n\
 \n\
 This Software was prepared for the Department of Homeland Security\n\
 (DHS) by the Battelle National Biodefense Institute, LLC (BNBI) as\n\

diff --git a/src/mash/CommandList.h b/src/mash/CommandList.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandPaste.cpp b/src/mash/CommandPaste.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandPaste.h b/src/mash/CommandPaste.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandSketch.cpp b/src/mash/CommandSketch.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/CommandSketch.h b/src/mash/CommandSketch.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/HashList.cpp b/src/mash/HashList.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/HashList.h b/src/mash/HashList.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/HashPriorityQueue.cpp b/src/mash/HashPriorityQueue.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/HashPriorityQueue.h b/src/mash/HashPriorityQueue.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/HashSet.cpp b/src/mash/HashSet.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/HashSet.h b/src/mash/HashSet.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/Sketch.cpp b/src/mash/Sketch.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/Sketch.h b/src/mash/Sketch.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/ThreadPool.h b/src/mash/ThreadPool.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/ThreadPool.hxx b/src/mash/ThreadPool.hxx
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/capnp/MinHash.capnp b/src/mash/capnp/MinHash.capnp
@@ -1,6 +1,6 @@
 # Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-# all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-# Adam Phillippy
+# all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+# Sergey Koren, and Adam Phillippy
 #
 # See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/hash.cpp b/src/mash/hash.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/hash.h b/src/mash/hash.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/mash.cpp b/src/mash/mash.cpp
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/memcpyLink.h b/src/mash/memcpyLink.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.
 

diff --git a/src/mash/version.h b/src/mash/version.h
@@ -1,6 +1,6 @@
 // Copyright © 2015, Battelle National Biodefense Institute (BNBI);
-// all rights reserved. Authored by: Brian Ondov, Todd Treangen, and
-// Adam Phillippy
+// all rights reserved. Authored by: Brian Ondov, Todd Treangen,
+// Sergey Koren, and Adam Phillippy
 //
 // See the LICENSE.txt file included with this software for license information.