From 3800e3508a79a7f6f5799bfa911639fe1dce33f0 Mon Sep 17 00:00:00 2001 From: Derrick Wood Date: Thu, 25 Apr 2019 00:01:33 -0400 Subject: [PATCH] Happy belated new year --- 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 +- 48 files changed, 51 insertions(+), 51 deletions(-) diff --git a/install_kraken2.sh b/install_kraken2.sh index 0cc4ea4..04fd753 100755 --- a/install_kraken2.sh +++ b/install_kraken2.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 b8a9edd..ba37d1f 100755 --- a/scripts/16S_gg_installation.sh +++ b/scripts/16S_gg_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 e883fc3..ca9c559 100755 --- a/scripts/16S_rdp_installation.sh +++ b/scripts/16S_rdp_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 ec6004f..fd9b0c7 100755 --- a/scripts/16S_silva_installation.sh +++ b/scripts/16S_silva_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 e4987e0..2e60b8e 100755 --- a/scripts/add_to_library.sh +++ b/scripts/add_to_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 f9e9930..eb4c66f 100755 --- a/scripts/build_gg_taxonomy.pl +++ b/scripts/build_gg_taxonomy.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 34e7ae9..e76122e 100755 --- a/scripts/build_kraken2_db.sh +++ b/scripts/build_kraken2_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 c9eab2b..7106b1b 100755 --- a/scripts/build_rdp_taxonomy.pl +++ b/scripts/build_rdp_taxonomy.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 956bae5..235ebfe 100755 --- a/scripts/build_silva_taxonomy.pl +++ b/scripts/build_silva_taxonomy.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 1972ab4..18fa6b6 100755 --- a/scripts/clean_db.sh +++ b/scripts/clean_db.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 9b0bd80..407b7da 100755 --- a/scripts/cp_into_tempfile.pl +++ b/scripts/cp_into_tempfile.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 af55fd7..c890d4e 100755 --- a/scripts/download_genomic_library.sh +++ b/scripts/download_genomic_library.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 ce90397..6fbae7b 100755 --- a/scripts/download_taxonomy.sh +++ b/scripts/download_taxonomy.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. diff --git a/scripts/kraken2 b/scripts/kraken2 index 844fdb2..b8a14e3 100755 --- a/scripts/kraken2 +++ b/scripts/kraken2 @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. @@ -216,7 +216,7 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013-2018, Derrick Wood (dwood\@cs.jhu.edu)\n"; + print "Copyright 2013-2019, Derrick Wood (dwood\@cs.jhu.edu)\n"; exit 0; } diff --git a/scripts/kraken2-build b/scripts/kraken2-build index 6cf12d6..62a082b 100755 --- a/scripts/kraken2-build +++ b/scripts/kraken2-build @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, Derrick Wood # # This file is part of the Kraken 2 taxonomic sequence classification system. @@ -235,7 +235,7 @@ sub display_help { sub display_version { print "Kraken version #####=VERSION=#####\n"; - print "Copyright 2013-2018, Derrick Wood (dwood\@cs.jhu.edu)\n"; + print "Copyright 2013-2019, Derrick Wood (dwood\@cs.jhu.edu)\n"; exit 0; } diff --git a/scripts/kraken2-inspect b/scripts/kraken2-inspect index 9f9d5fa..7d52d7b 100755 --- a/scripts/kraken2-inspect +++ b/scripts/kraken2-inspect @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 2013-2018, Derrick Wood (dwood\@cs.jhu.edu)\n"; + print "Copyright 2013-2019, Derrick Wood (dwood\@cs.jhu.edu)\n"; exit 0; } diff --git a/scripts/kraken2lib.pm b/scripts/kraken2lib.pm index e890170..44698bc 100644 --- a/scripts/kraken2lib.pm +++ b/scripts/kraken2lib.pm @@ -1,6 +1,6 @@ package kraken2lib; -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 1f2ee1b..042b494 100755 --- a/scripts/lookup_accession_numbers.pl +++ b/scripts/lookup_accession_numbers.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 bece9b9..efa0140 100755 --- a/scripts/make_seqid2taxid_map.pl +++ b/scripts/make_seqid2taxid_map.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 e35151c..d0a003e 100755 --- a/scripts/mask_low_complexity.sh +++ b/scripts/mask_low_complexity.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 506a654..ffacce5 100755 --- a/scripts/rsync_from_ncbi.pl +++ b/scripts/rsync_from_ncbi.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 1976773..d80c41a 100755 --- a/scripts/scan_fasta_file.pl +++ b/scripts/scan_fasta_file.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 5186750..b7cd261 100755 --- a/scripts/standard_installation.sh +++ b/scripts/standard_installation.sh @@ -1,6 +1,6 @@ #!/bin/bash -# Copyright 2013-2018, Derrick Wood +# Copyright 2013-2019, 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 23e62e6..e522a85 100644 --- a/src/aa_translate.cc +++ b/src/aa_translate.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 17985b9..c849c6a 100644 --- a/src/aa_translate.h +++ b/src/aa_translate.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 2f7c4b5..89d3bc7 100644 --- a/src/build_db.cc +++ b/src/build_db.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 b493143..55d3913 100644 --- a/src/classify.cc +++ b/src/classify.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 c0c4748..0040541 100644 --- a/src/compact_hash.cc +++ b/src/compact_hash.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 a94a7bf..e56f92b 100644 --- a/src/compact_hash.h +++ b/src/compact_hash.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 5618004..7ea9e91 100644 --- a/src/dump_table.cc +++ b/src/dump_table.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 e6f647d..cd02a47 100644 --- a/src/estimate_capacity.cc +++ b/src/estimate_capacity.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 ee4dccf..b8dd263 100644 --- a/src/kraken2_data.h +++ b/src/kraken2_data.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 4109c1c..b0c67d2 100644 --- a/src/kv_store.h +++ b/src/kv_store.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 cde2c5b..eca9006 100644 --- a/src/lookup_accession_numbers.cc +++ b/src/lookup_accession_numbers.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 0efcf94..0655082 100644 --- a/src/mmap_file.cc +++ b/src/mmap_file.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 5a6b92a..bb1b36b 100644 --- a/src/mmap_file.h +++ b/src/mmap_file.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 fec65b3..73e8e7f 100644 --- a/src/mmscanner.cc +++ b/src/mmscanner.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 8d860a6..186c1e2 100644 --- a/src/mmscanner.h +++ b/src/mmscanner.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 aefd0d0..520b89f 100644 --- a/src/omp_hack.cc +++ b/src/omp_hack.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 c5be053..3ab9925 100644 --- a/src/omp_hack.h +++ b/src/omp_hack.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 94a6a7d..12512e3 100644 --- a/src/reports.cc +++ b/src/reports.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 22cbbfc..800ca33 100644 --- a/src/reports.h +++ b/src/reports.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 2df1beb..44eb34b 100644 --- a/src/seqreader.cc +++ b/src/seqreader.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 fc0d983..42f97fb 100644 --- a/src/seqreader.h +++ b/src/seqreader.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 fc77a15..e66964d 100644 --- a/src/taxonomy.cc +++ b/src/taxonomy.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 571f5c9..06184a3 100644 --- a/src/taxonomy.h +++ b/src/taxonomy.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 20dbaaa..6d7eff7 100644 --- a/src/utilities.cc +++ b/src/utilities.cc @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, 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 eeb2273..44d9941 100644 --- a/src/utilities.h +++ b/src/utilities.h @@ -1,5 +1,5 @@ /* - * Copyright 2013-2018, Derrick Wood + * Copyright 2013-2019, Derrick Wood * * This file is part of the Kraken 2 taxonomic sequence classification system. */