diff --git a/bam.c b/bam.c index e50515eea..926062c71 100644 --- a/bam.c +++ b/bam.c @@ -1,6 +1,6 @@ /* bam.c -- BAM format. - Copyright (C) 2008-2013, 2015, 2019 Genome Research Ltd. + Copyright (C) 2008-2013, 2015, 2019-2020 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li diff --git a/bam2depth.c b/bam2depth.c index 4f92990f1..113bdadee 100644 --- a/bam2depth.c +++ b/bam2depth.c @@ -1,7 +1,7 @@ /* bam2depth.c -- depth subcommand. Copyright (C) 2011, 2012 Broad Institute. - Copyright (C) 2012-2016, 2018, 2019 Genome Research Ltd. + Copyright (C) 2012-2016, 2018, 2019-2020 Genome Research Ltd. Author: Heng Li diff --git a/bam_addrprg.c b/bam_addrprg.c index 26cdcc035..9456d5d76 100644 --- a/bam_addrprg.c +++ b/bam_addrprg.c @@ -1,6 +1,6 @@ /* bam_addrprg.c -- samtools command to add or replace readgroups. - Copyright (c) 2013, 2015-2017, 2019 Genome Research Limited. + Copyright (c) 2013, 2015-2017, 2019-2020 Genome Research Limited. Author: Martin O. Pollard diff --git a/bam_markdup.c b/bam_markdup.c index 8b56e7bcd..edb491959 100644 --- a/bam_markdup.c +++ b/bam_markdup.c @@ -1,7 +1,7 @@ /* bam_markdup.c -- Mark duplicates from a coord sorted file that has gone through fixmates with the mate scoring option on. - Copyright (C) 2017-2019 Genome Research Ltd. + Copyright (C) 2017-2020 Genome Research Ltd. Author: Andrew Whitwham diff --git a/bam_md.c b/bam_md.c index 0a42df7f5..7d5aeaaf4 100644 --- a/bam_md.c +++ b/bam_md.c @@ -1,6 +1,6 @@ /* bam_md.c -- calmd subcommand. - Copyright (C) 2009-2011, 2014-2015, 2019 Genome Research Ltd. + Copyright (C) 2009-2011, 2014-2015, 2019-2020 Genome Research Ltd. Portions copyright (C) 2009-2011 Broad Institute. Author: Heng Li diff --git a/bam_plcmd.c b/bam_plcmd.c index 518614273..17a0e95cc 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -1,6 +1,6 @@ /* bam_plcmd.c -- mpileup subcommand. - Copyright (C) 2008-2015, 2019 Genome Research Ltd. + Copyright (C) 2008-2015, 2019-2020 Genome Research Ltd. Portions copyright (C) 2009-2012 Broad Institute. Author: Heng Li diff --git a/bam_tview.c b/bam_tview.c index 84e5ac6a3..4ba45453a 100644 --- a/bam_tview.c +++ b/bam_tview.c @@ -1,6 +1,6 @@ /* bam_tview.c -- tview subcommand. - Copyright (C) 2008-2016, 2019 Genome Research Ltd. + Copyright (C) 2008-2016, 2019-2020 Genome Research Ltd. Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes. Author: Heng Li diff --git a/bamtk.c b/bamtk.c index fbf093fa9..1af399310 100644 --- a/bamtk.c +++ b/bamtk.c @@ -214,7 +214,7 @@ int main(int argc, char *argv[]) printf( "samtools %s\n" "Using htslib %s\n" -"Copyright (C) 2019 Genome Research Ltd.\n", +"Copyright (C) 2019-2020 Genome Research Ltd.\n", samtools_version(), hts_version()); } else if (strcmp(argv[1], "--version-only") == 0) { diff --git a/configure.ac b/configure.ac index 2d1492434..cbf057c0d 100644 --- a/configure.ac +++ b/configure.ac @@ -1,6 +1,6 @@ # Configure script for samtools, utilities for Sequence Alignment/Map files. # -# Copyright (C) 2015, 2017 Genome Research Ltd. +# Copyright (C) 2015, 2017, 2019 Genome Research Ltd. # # Author: John Marshall # diff --git a/dict.c b/dict.c index cff3d49ce..029d54876 100644 --- a/dict.c +++ b/dict.c @@ -1,6 +1,6 @@ /* dict.c -- create a sequence dictionary file. - Copyright (C) 2015 Genome Research Ltd. + Copyright (C) 2015, 2020 Genome Research Ltd. Author: Shane McCarthy diff --git a/doc/samtools-addreplacerg.1 b/doc/samtools-addreplacerg.1 index c913609f9..f0eaeaae0 100644 --- a/doc/samtools-addreplacerg.1 +++ b/doc/samtools-addreplacerg.1 @@ -3,7 +3,7 @@ .SH NAME samtools addreplacerg \- adds or replaces read group tags .\" -.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2018, 2020 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-bedcov.1 b/doc/samtools-bedcov.1 index d9fca5a74..d6bcefd3c 100644 --- a/doc/samtools-bedcov.1 +++ b/doc/samtools-bedcov.1 @@ -3,7 +3,7 @@ .SH NAME samtools bedcov \- reports coverage over regions in a supplied BED file .\" -.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2018, 2020 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-depth.1 b/doc/samtools-depth.1 index daa58da85..d11829fdd 100644 --- a/doc/samtools-depth.1 +++ b/doc/samtools-depth.1 @@ -3,7 +3,7 @@ .SH NAME samtools depth \- computes the read depth at each position or region .\" -.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2020 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-fasta.1 b/doc/samtools-fasta.1 index cb646976f..c17ec1285 100644 --- a/doc/samtools-fasta.1 +++ b/doc/samtools-fasta.1 @@ -3,7 +3,7 @@ .SH NAME samtools fasta / fastq \- converts a SAM/BAM/CRAM file to FASTA or FASTQ .\" -.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2020 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-index.1 b/doc/samtools-index.1 index 7f6635250..36fa20b76 100644 --- a/doc/samtools-index.1 +++ b/doc/samtools-index.1 @@ -3,7 +3,7 @@ .SH NAME samtools index \- indexes SAM/BAM/CRAM files .\" -.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-markdup.1 b/doc/samtools-markdup.1 index 5035d9545..0723139bd 100644 --- a/doc/samtools-markdup.1 +++ b/doc/samtools-markdup.1 @@ -3,7 +3,7 @@ .SH NAME samtools markdup \- mark duplicate alignments in a coordinate sorted file .\" -.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2020 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-merge.1 b/doc/samtools-merge.1 index bd119bd2c..5a6ddf4b4 100644 --- a/doc/samtools-merge.1 +++ b/doc/samtools-merge.1 @@ -3,7 +3,7 @@ .SH NAME samtools merge \- merges multiple sorted input files into a single output. .\" -.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-mpileup.1 b/doc/samtools-mpileup.1 index afba4e0d9..844582bdd 100644 --- a/doc/samtools-mpileup.1 +++ b/doc/samtools-mpileup.1 @@ -3,7 +3,7 @@ .SH NAME samtools mpileup \- produces "pileup" textual format from an alignment .\" -.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2020 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-sort.1 b/doc/samtools-sort.1 index a85db8707..529077a61 100644 --- a/doc/samtools-sort.1 +++ b/doc/samtools-sort.1 @@ -3,7 +3,7 @@ .SH NAME samtools sort \- sorts SAM/BAM/CRAM files .\" -.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/doc/samtools-view.1 b/doc/samtools-view.1 index 3cbe4462a..566295969 100644 --- a/doc/samtools-view.1 +++ b/doc/samtools-view.1 @@ -3,7 +3,7 @@ .SH NAME samtools view \- views and converts SAM/BAM/CRAM files .\" -.\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. +.\" Copyright (C) 2008-2011, 2013-2020 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li diff --git a/misc/blast2sam.pl b/misc/blast2sam.pl index 6057530bc..7318cbe4e 100755 --- a/misc/blast2sam.pl +++ b/misc/blast2sam.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl # -# Copyright (C) 2009 Genome Research Ltd. +# Copyright (C) 2009, 2014 Genome Research Ltd. # Portions copyright (C) 2014 Ontario Institute for Cancer Research. # # Author: Heng Li diff --git a/misc/export2sam.pl b/misc/export2sam.pl index de0fba608..c6b5d2bb3 100755 --- a/misc/export2sam.pl +++ b/misc/export2sam.pl @@ -9,7 +9,7 @@ # # The MIT License # -# Copyright (c) 2008-2009 Genome Research Ltd. +# Copyright (c) 2008-2010 Genome Research Ltd. # Modifications Copyright (c) 2010 Illumina, Inc. # # Permission is hereby granted, free of charge, to any person obtaining a copy diff --git a/misc/md5fa.c b/misc/md5fa.c index bdeba586f..e0cda6ff6 100644 --- a/misc/md5fa.c +++ b/misc/md5fa.c @@ -1,6 +1,6 @@ /* md5fa.c -- MD5 checksum utility. - Copyright (C) 2008, 2009 Genome Research Ltd. + Copyright (C) 2008, 2009, 2015 Genome Research Ltd. Author: Heng Li diff --git a/misc/md5sum-lite.c b/misc/md5sum-lite.c index c3e44d43d..e17a65447 100644 --- a/misc/md5sum-lite.c +++ b/misc/md5sum-lite.c @@ -1,6 +1,6 @@ /* md5sum-lite.c -- Basic md5sum implementation. - Copyright (C) 2008, 2009 Genome Research Ltd. + Copyright (C) 2008, 2009, 2015 Genome Research Ltd. Author: Heng Li diff --git a/misc/wgsim_eval.pl b/misc/wgsim_eval.pl index 7e4fa9417..4e12c8639 100755 --- a/misc/wgsim_eval.pl +++ b/misc/wgsim_eval.pl @@ -1,6 +1,6 @@ #!/usr/bin/env perl # -# Copyright (C) 2009 Genome Research Ltd. +# Copyright (C) 2009, 2015 Genome Research Ltd. # Portions copyright (C) 2009-2011 Broad Institute. # # Author: Heng Li diff --git a/padding.c b/padding.c index c5819c96c..11b098ec1 100644 --- a/padding.c +++ b/padding.c @@ -1,7 +1,7 @@ /* padding.c -- depad subcommand. Copyright (C) 2011, 2012 Broad Institute. - Copyright (C) 2014-2016, 2019 Genome Research Ltd. + Copyright (C) 2014-2016, 2019-2020 Genome Research Ltd. Portions copyright (C) 2012, 2013 Peter Cock, The James Hutton Institute. Author: Heng Li diff --git a/sam_view.c b/sam_view.c index 3720f4024..18da116fb 100644 --- a/sam_view.c +++ b/sam_view.c @@ -1,6 +1,6 @@ /* sam_view.c -- SAM<->BAM<->CRAM conversion. - Copyright (C) 2009-2019 Genome Research Ltd. + Copyright (C) 2009-2020 Genome Research Ltd. Portions copyright (C) 2009, 2011, 2012 Broad Institute. Author: Heng Li diff --git a/test/merge/test_bam_translate.c b/test/merge/test_bam_translate.c index ec2f18bd5..5e723f1b9 100644 --- a/test/merge/test_bam_translate.c +++ b/test/merge/test_bam_translate.c @@ -1,6 +1,6 @@ /* test/merge/test_bam_translate.c -- header merging test harness. - Copyright (C) 2013, 2014 Genome Research Ltd. + Copyright (C) 2013, 2014-2015 Genome Research Ltd. Author: Martin O. Pollard diff --git a/test/mpileup/regression.sh b/test/mpileup/regression.sh index 7989ed904..fb0e3b5cb 100755 --- a/test/mpileup/regression.sh +++ b/test/mpileup/regression.sh @@ -1,6 +1,6 @@ #!/bin/sh # -# Copyright (C) 2014 Genome Research Ltd. +# Copyright (C) 2014-2015 Genome Research Ltd. # # Author: James Bonfield # diff --git a/test/split/test_expand_format_string.c b/test/split/test_expand_format_string.c index 962d7cdc3..91e8e69ca 100644 --- a/test/split/test_expand_format_string.c +++ b/test/split/test_expand_format_string.c @@ -1,6 +1,6 @@ /* test/split/test_expand_format_string.c -- split format string test cases. - Copyright (C) 2014 Genome Research Ltd. + Copyright (C) 2014-2015 Genome Research Ltd. Author: Martin O. Pollard diff --git a/test/split/test_parse_args.c b/test/split/test_parse_args.c index 85a196ac8..a49472e00 100644 --- a/test/split/test_parse_args.c +++ b/test/split/test_parse_args.c @@ -1,6 +1,6 @@ /* test/split/test_parse_args.c -- split test cases. - Copyright (C) 2014 Genome Research Ltd. + Copyright (C) 2014-2015 Genome Research Ltd. Author: Martin O. Pollard diff --git a/test/stat/11.stats.targets b/test/stat/11.stats.targets index 886413841..93750a418 100644 --- a/test/stat/11.stats.targets +++ b/test/stat/11.stats.targets @@ -1,6 +1,6 @@ # The MIT License # -# Copyright (c) 2014 Genome Research Ltd. +# Copyright (c) 2014, 2018 Genome Research Ltd. # # 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/test/vcf-miniview.c b/test/vcf-miniview.c index e6346f30b..ba4133517 100644 --- a/test/vcf-miniview.c +++ b/test/vcf-miniview.c @@ -1,6 +1,6 @@ /* test/vcf-miniview.c -- minimal BCF/VCF viewer, for use by test harness. - Copyright (C) 2014 Genome Research Ltd. + Copyright (C) 2014, 2016 Genome Research Ltd. Author: John Marshall