From 383ef55774954b4684064d9e4003f64708b66fc4 Mon Sep 17 00:00:00 2001 From: Derrick Wood Date: Tue, 6 Jun 2023 18:42:30 -0400 Subject: [PATCH] Copyright update --- LICENSE | 2 +- install_kraken2.sh | 2 +- scripts/16S_gg_installation.sh | 2 +- scripts/16S_rdp_installation.sh | 2 +- scripts/16S_silva_installation.sh | 2 +- scripts/add_to_library.sh | 2 +- scripts/build_gg_taxonomy.pl | 2 +- scripts/build_kraken2_db.sh | 2 +- scripts/build_rdp_taxonomy.pl | 2 +- scripts/build_silva_taxonomy.pl | 2 +- scripts/clean_db.sh | 2 +- scripts/cp_into_tempfile.pl | 2 +- scripts/download_genomic_library.sh | 2 +- scripts/download_taxonomy.sh | 2 +- scripts/kraken2 | 4 ++-- scripts/kraken2-build | 4 ++-- scripts/kraken2-inspect | 4 ++-- scripts/kraken2lib.pm | 2 +- scripts/lookup_accession_numbers.pl | 2 +- scripts/make_seqid2taxid_map.pl | 2 +- scripts/mask_low_complexity.sh | 2 +- scripts/rsync_from_ncbi.pl | 2 +- scripts/scan_fasta_file.pl | 2 +- scripts/standard_installation.sh | 2 +- src/aa_translate.cc | 2 +- src/aa_translate.h | 2 +- src/build_db.cc | 2 +- src/classify.cc | 2 +- src/compact_hash.cc | 2 +- src/compact_hash.h | 2 +- src/dump_table.cc | 2 +- src/estimate_capacity.cc | 2 +- src/kraken2_data.h | 2 +- src/kv_store.h | 2 +- src/lookup_accession_numbers.cc | 2 +- src/mmap_file.cc | 2 +- src/mmap_file.h | 2 +- src/mmscanner.cc | 2 +- src/mmscanner.h | 2 +- src/omp_hack.cc | 2 +- src/omp_hack.h | 2 +- src/reports.cc | 2 +- src/reports.h | 2 +- src/seqreader.cc | 2 +- src/seqreader.h | 2 +- src/taxonomy.cc | 2 +- src/taxonomy.h | 2 +- src/utilities.cc | 2 +- src/utilities.h | 2 +- 49 files changed, 52 insertions(+), 52 deletions(-) diff --git a/LICENSE b/LICENSE index 2948193..cd11f22 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ The MIT License (MIT) -Copyright (c) 2017-2021 Derrick Wood +Copyright (c) 2017-2023 Derrick Wood Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/install_kraken2.sh b/install_kraken2.sh index 891fde2..bc65170 100755 --- a/install_kraken2.sh +++ b/install_kraken2.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/16S_gg_installation.sh b/scripts/16S_gg_installation.sh index 4f70ed7..e3ec46d 100755 --- a/scripts/16S_gg_installation.sh +++ b/scripts/16S_gg_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/16S_rdp_installation.sh b/scripts/16S_rdp_installation.sh index cc57f02..a4acc74 100755 --- a/scripts/16S_rdp_installation.sh +++ b/scripts/16S_rdp_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/16S_silva_installation.sh b/scripts/16S_silva_installation.sh index 0573c08..b88d4f4 100755 --- a/scripts/16S_silva_installation.sh +++ b/scripts/16S_silva_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/add_to_library.sh b/scripts/add_to_library.sh index a00fa30..23560d4 100755 --- a/scripts/add_to_library.sh +++ b/scripts/add_to_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/build_gg_taxonomy.pl b/scripts/build_gg_taxonomy.pl index 421d1ef..260f009 100755 --- a/scripts/build_gg_taxonomy.pl +++ b/scripts/build_gg_taxonomy.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/build_kraken2_db.sh b/scripts/build_kraken2_db.sh index a5dfa1e..bc83218 100755 --- a/scripts/build_kraken2_db.sh +++ b/scripts/build_kraken2_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/build_rdp_taxonomy.pl b/scripts/build_rdp_taxonomy.pl index 304e305..72223c9 100755 --- a/scripts/build_rdp_taxonomy.pl +++ b/scripts/build_rdp_taxonomy.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/build_silva_taxonomy.pl b/scripts/build_silva_taxonomy.pl index ae4641c..ca4422c 100755 --- a/scripts/build_silva_taxonomy.pl +++ b/scripts/build_silva_taxonomy.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/clean_db.sh b/scripts/clean_db.sh index cbe3612..c701897 100755 --- a/scripts/clean_db.sh +++ b/scripts/clean_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/cp_into_tempfile.pl b/scripts/cp_into_tempfile.pl index a2961b2..ff40098 100755 --- a/scripts/cp_into_tempfile.pl +++ b/scripts/cp_into_tempfile.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/download_genomic_library.sh b/scripts/download_genomic_library.sh index ffd96d2..4459598 100755 --- a/scripts/download_genomic_library.sh +++ b/scripts/download_genomic_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/download_taxonomy.sh b/scripts/download_taxonomy.sh index 85fc7d2..edef180 100755 --- a/scripts/download_taxonomy.sh +++ b/scripts/download_taxonomy.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/kraken2 b/scripts/kraken2 index af8376d..d1e81d1 100755 --- a/scripts/kraken2 +++ b/scripts/kraken2 @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. @@ -231,7 +231,7 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013-2021, Derrick Wood (dwood\@cs.jhu.edu)\n"; + print "Copyright 2013-2023, Derrick Wood (dwood\@cs.jhu.edu)\n"; exit 0; } diff --git a/scripts/kraken2-build b/scripts/kraken2-build index def924b..b27e3da 100755 --- a/scripts/kraken2-build +++ b/scripts/kraken2-build @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. @@ -282,7 +282,7 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013-2021, Derrick Wood (dwood\@cs.jhu.edu)\n"; + print "Copyright 2013-2023, Derrick Wood (dwood\@cs.jhu.edu)\n"; exit 0; } diff --git a/scripts/kraken2-inspect b/scripts/kraken2-inspect index b38037b..cda9de1 100755 --- a/scripts/kraken2-inspect +++ b/scripts/kraken2-inspect @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. @@ -105,6 +105,6 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013-2021, Derrick Wood (dwood\@cs.jhu.edu)\n"; + print "Copyright 2013-2023, Derrick Wood (dwood\@cs.jhu.edu)\n"; exit 0; } diff --git a/scripts/kraken2lib.pm b/scripts/kraken2lib.pm index d84ce80..dd6e745 100644 --- a/scripts/kraken2lib.pm +++ b/scripts/kraken2lib.pm @@ -1,6 +1,6 @@ package kraken2lib; -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/lookup_accession_numbers.pl b/scripts/lookup_accession_numbers.pl index cc65efd..17ce802 100755 --- a/scripts/lookup_accession_numbers.pl +++ b/scripts/lookup_accession_numbers.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/make_seqid2taxid_map.pl b/scripts/make_seqid2taxid_map.pl index 1a51ef5..53a2246 100755 --- a/scripts/make_seqid2taxid_map.pl +++ b/scripts/make_seqid2taxid_map.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/mask_low_complexity.sh b/scripts/mask_low_complexity.sh index 9152efa..23b3154 100755 --- a/scripts/mask_low_complexity.sh +++ b/scripts/mask_low_complexity.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/rsync_from_ncbi.pl b/scripts/rsync_from_ncbi.pl index 7069488..bc26c15 100755 --- a/scripts/rsync_from_ncbi.pl +++ b/scripts/rsync_from_ncbi.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/scan_fasta_file.pl b/scripts/scan_fasta_file.pl index a3c2db9..6432491 100755 --- a/scripts/scan_fasta_file.pl +++ b/scripts/scan_fasta_file.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/standard_installation.sh b/scripts/standard_installation.sh index 97c928a..a529256 100755 --- a/scripts/standard_installation.sh +++ b/scripts/standard_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2021, Derrick Wood +# Copyright 2013-2023, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/src/aa_translate.cc b/src/aa_translate.cc index 808c3c1..4c89e5a 100644 --- a/src/aa_translate.cc +++ b/src/aa_translate.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/aa_translate.h b/src/aa_translate.h index 7cd2ced..a919519 100644 --- a/src/aa_translate.h +++ b/src/aa_translate.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/build_db.cc b/src/build_db.cc index 5d829ee..7434149 100644 --- a/src/build_db.cc +++ b/src/build_db.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/classify.cc b/src/classify.cc index e01e554..012db34 100644 --- a/src/classify.cc +++ b/src/classify.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/compact_hash.cc b/src/compact_hash.cc index 2a703e6..effb8c9 100644 --- a/src/compact_hash.cc +++ b/src/compact_hash.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/compact_hash.h b/src/compact_hash.h index c70c4ec..9e7eeb1 100644 --- a/src/compact_hash.h +++ b/src/compact_hash.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/dump_table.cc b/src/dump_table.cc index b599da4..bc0c811 100644 --- a/src/dump_table.cc +++ b/src/dump_table.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/estimate_capacity.cc b/src/estimate_capacity.cc index 7be7342..4a4dd5a 100644 --- a/src/estimate_capacity.cc +++ b/src/estimate_capacity.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/kraken2_data.h b/src/kraken2_data.h index 9690e34..627fe33 100644 --- a/src/kraken2_data.h +++ b/src/kraken2_data.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/kv_store.h b/src/kv_store.h index 5948fba..57a1836 100644 --- a/src/kv_store.h +++ b/src/kv_store.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/lookup_accession_numbers.cc b/src/lookup_accession_numbers.cc index b422e19..200fe72 100644 --- a/src/lookup_accession_numbers.cc +++ b/src/lookup_accession_numbers.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/mmap_file.cc b/src/mmap_file.cc index 4df997b..4940a34 100644 --- a/src/mmap_file.cc +++ b/src/mmap_file.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/mmap_file.h b/src/mmap_file.h index 50ce747..9dca4d7 100644 --- a/src/mmap_file.h +++ b/src/mmap_file.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/mmscanner.cc b/src/mmscanner.cc index c371137..a7754b4 100644 --- a/src/mmscanner.cc +++ b/src/mmscanner.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/mmscanner.h b/src/mmscanner.h index 3271b67..18e89cd 100644 --- a/src/mmscanner.h +++ b/src/mmscanner.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/omp_hack.cc b/src/omp_hack.cc index 2ac3202..6b6801d 100644 --- a/src/omp_hack.cc +++ b/src/omp_hack.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/omp_hack.h b/src/omp_hack.h index 72d8d5a..fad7a14 100644 --- a/src/omp_hack.h +++ b/src/omp_hack.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/reports.cc b/src/reports.cc index 00bd5e4..1af75ac 100644 --- a/src/reports.cc +++ b/src/reports.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/reports.h b/src/reports.h index 7948e32..557c6f9 100644 --- a/src/reports.h +++ b/src/reports.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/seqreader.cc b/src/seqreader.cc index 075a994..5d9a2c1 100644 --- a/src/seqreader.cc +++ b/src/seqreader.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/seqreader.h b/src/seqreader.h index cae9c4f..c61c4d8 100644 --- a/src/seqreader.h +++ b/src/seqreader.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/taxonomy.cc b/src/taxonomy.cc index 336d25f..605ae9e 100644 --- a/src/taxonomy.cc +++ b/src/taxonomy.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/taxonomy.h b/src/taxonomy.h index 4e69d18..36b7af3 100644 --- a/src/taxonomy.h +++ b/src/taxonomy.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/utilities.cc b/src/utilities.cc index 849b7cd..26ca62f 100644 --- a/src/utilities.cc +++ b/src/utilities.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */ diff --git a/src/utilities.h b/src/utilities.h index e0370bb..6c26440 100644 --- a/src/utilities.h +++ b/src/utilities.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2021, Derrick Wood + * Copyright 2013-2023, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */