From 54af2068589552ac86254e7af88e2f89f4e92bc9 Mon Sep 17 00:00:00 2001 From: Derrick Wood Date: Sat, 4 Jan 2014 13:17:07 -0500 Subject: [PATCH] copyright updates, prep for release --- README | 10 +++++----- install_kraken.sh | 2 +- scripts/add_to_library.sh | 2 +- scripts/build_kraken_db.sh | 2 +- scripts/clean_db.sh | 2 +- scripts/download_genomic_library.sh | 2 +- scripts/download_taxonomy.sh | 2 +- scripts/kraken-build.broken | 4 ++-- scripts/kraken-report.broken | 4 ++-- scripts/kraken.broken | 4 ++-- scripts/shrink_db.sh | 2 +- scripts/standard_installation.sh | 2 +- scripts/upgrade_db.sh | 2 +- src/classify.cpp | 2 +- src/db_shrink.cpp | 2 +- src/db_sort.cpp | 2 +- src/krakendb.cpp | 2 +- src/krakendb.hpp | 2 +- src/krakenutil.cpp | 2 +- src/krakenutil.hpp | 2 +- src/make_file_to_taxon_map.cpp | 2 +- src/quickfile.cpp | 2 +- src/quickfile.hpp | 2 +- src/seqreader.cpp | 2 +- src/seqreader.hpp | 2 +- src/set_lcas.cpp | 2 +- 26 files changed, 33 insertions(+), 33 deletions(-) diff --git a/README b/README index ef01a95..be67a12 100644 --- a/README +++ b/README @@ -172,12 +172,12 @@ have multi-threading enabled) in December 2013: 10m50s *Step 1 (create set) n/a Step 2 (reduce database, optional and skipped) - 21m24s *Step 3 (sort set) - 0m47s Step 4 (GI number to file map) - 0m58s Step 5 (File to taxon map) - 39m10s *Step 6 (set LCA values) + 24m10s *Step 3 (sort set) + 1m28s Step 4 (GI number to file map) + 1m10s Step 5 (File to taxon map) + 47m08s *Step 6 (set LCA values) ------ - 73m10s Total build time + 84m47s Total build time To create a custom database, or to use a database from another source, see CUSTOM DATABASES. diff --git a/install_kraken.sh b/install_kraken.sh index 8e0674f..1820f84 100755 --- a/install_kraken.sh +++ b/install_kraken.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic classification system. # diff --git a/scripts/add_to_library.sh b/scripts/add_to_library.sh index fa25dc6..2c2b7fd 100755 --- a/scripts/add_to_library.sh +++ b/scripts/add_to_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/build_kraken_db.sh b/scripts/build_kraken_db.sh index c9a29dd..37152f2 100755 --- a/scripts/build_kraken_db.sh +++ b/scripts/build_kraken_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/clean_db.sh b/scripts/clean_db.sh index 84bf208..ba91f1d 100755 --- a/scripts/clean_db.sh +++ b/scripts/clean_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/download_genomic_library.sh b/scripts/download_genomic_library.sh index d567b22..64b5143 100755 --- a/scripts/download_genomic_library.sh +++ b/scripts/download_genomic_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/download_taxonomy.sh b/scripts/download_taxonomy.sh index 2b35a86..7c28c0c 100755 --- a/scripts/download_taxonomy.sh +++ b/scripts/download_taxonomy.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/kraken-build.broken b/scripts/kraken-build.broken index 5f15d15..af4ace9 100755 --- a/scripts/kraken-build.broken +++ b/scripts/kraken-build.broken @@ -1,6 +1,6 @@ #!/usr/bin/perl -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # @@ -235,7 +235,7 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n"; + print "Copyright 2013-2014, Derrick Wood (dwood\@cs.umd.edu)\n"; exit 0; } diff --git a/scripts/kraken-report.broken b/scripts/kraken-report.broken index 9337501..4ec304c 100755 --- a/scripts/kraken-report.broken +++ b/scripts/kraken-report.broken @@ -1,6 +1,6 @@ #!/usr/bin/perl -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # @@ -42,7 +42,7 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n"; + print "Copyright 2013-2014, Derrick Wood (dwood\@cs.umd.edu)\n"; exit 0; } diff --git a/scripts/kraken.broken b/scripts/kraken.broken index af036c1..399ac03 100755 --- a/scripts/kraken.broken +++ b/scripts/kraken.broken @@ -1,6 +1,6 @@ #!/usr/bin/perl -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # @@ -128,6 +128,6 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013, Derrick Wood (dwood\@cs.umd.edu)\n"; + print "Copyright 2013-2014, Derrick Wood (dwood\@cs.umd.edu)\n"; exit 0; } diff --git a/scripts/shrink_db.sh b/scripts/shrink_db.sh index b247eed..56ae6c9 100755 --- a/scripts/shrink_db.sh +++ b/scripts/shrink_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh index b97fb9e..d19c41e 100755 --- a/scripts/standard_installation.sh +++ b/scripts/standard_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/scripts/upgrade_db.sh b/scripts/upgrade_db.sh index 211e4f3..9d9e094 100755 --- a/scripts/upgrade_db.sh +++ b/scripts/upgrade_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013, Derrick Wood +# Copyright 2013-2014, Derrick Wood # # This file is part of the Kraken taxonomic sequence classification system. # diff --git a/src/classify.cpp b/src/classify.cpp index f312c58..1f0c614 100644 --- a/src/classify.cpp +++ b/src/classify.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/db_shrink.cpp b/src/db_shrink.cpp index abb4f58..56eecbd 100644 --- a/src/db_shrink.cpp +++ b/src/db_shrink.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/db_sort.cpp b/src/db_sort.cpp index 1d87d5a..8d43cdf 100644 --- a/src/db_sort.cpp +++ b/src/db_sort.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakendb.cpp b/src/krakendb.cpp index d9088cb..c6d184b 100644 --- a/src/krakendb.cpp +++ b/src/krakendb.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakendb.hpp b/src/krakendb.hpp index dc44096..bfd84a7 100644 --- a/src/krakendb.hpp +++ b/src/krakendb.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakenutil.cpp b/src/krakenutil.cpp index d73e4bb..c64b00f 100644 --- a/src/krakenutil.cpp +++ b/src/krakenutil.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/krakenutil.hpp b/src/krakenutil.hpp index e8b1f4b..a239d4e 100644 --- a/src/krakenutil.hpp +++ b/src/krakenutil.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/make_file_to_taxon_map.cpp b/src/make_file_to_taxon_map.cpp index f3d9c0d..2c53305 100644 --- a/src/make_file_to_taxon_map.cpp +++ b/src/make_file_to_taxon_map.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/quickfile.cpp b/src/quickfile.cpp index d5662d0..32168e0 100644 --- a/src/quickfile.cpp +++ b/src/quickfile.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/quickfile.hpp b/src/quickfile.hpp index c713ce9..2ab4964 100644 --- a/src/quickfile.hpp +++ b/src/quickfile.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/seqreader.cpp b/src/seqreader.cpp index d090dd8..79783eb 100644 --- a/src/seqreader.cpp +++ b/src/seqreader.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/seqreader.hpp b/src/seqreader.hpp index 276e87b..d602e3c 100644 --- a/src/seqreader.hpp +++ b/src/seqreader.hpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. * diff --git a/src/set_lcas.cpp b/src/set_lcas.cpp index 7608463..256151a 100644 --- a/src/set_lcas.cpp +++ b/src/set_lcas.cpp @@ -1,5 +1,5 @@ /* - * Copyright 2013, Derrick Wood + * Copyright 2013-2014, Derrick Wood * * This file is part of the Kraken taxonomic sequence classification system. *