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Updates copyright message for 2019.
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Added 2019 to copyright dates on files committed in 2019.

Update files that should have been done before 2019.
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@whitwham @daviesrob
whitwham authored and daviesrob committed Nov 12, 2019
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2 changes: 1 addition & 1 deletion Makefile
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# Makefile for samtools, utilities for the Sequence Alignment/Map format.
#
# Copyright (C) 2008-2017 Genome Research Ltd.
# Copyright (C) 2008-2019 Genome Research Ltd.
# Portions copyright (C) 2010-2012 Broad Institute.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
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2 changes: 1 addition & 1 deletion bam.c
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/* bam.c -- BAM format.
Copyright (C) 2008-2013, 2015 Genome Research Ltd.
Copyright (C) 2008-2013, 2015, 2019 Genome Research Ltd.
Portions copyright (C) 2009-2012 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam.h
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/* bam.h -- BAM API.
Copyright (C) 2008-2014 Genome Research Ltd.
Copyright (C) 2008-2014, 2019 Genome Research Ltd.
Portions copyright (C) 2010-2012 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam2bcf.c
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/* bam2bcf.c -- variant calling.
Copyright (C) 2010-2012 Broad Institute.
Copyright (C) 2012-2014 Genome Research Ltd.
Copyright (C) 2012-2015 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam2depth.c
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/* bam2depth.c -- depth subcommand.
Copyright (C) 2011, 2012 Broad Institute.
Copyright (C) 2012-2014 Genome Research Ltd.
Copyright (C) 2012-2016, 2018, 2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_addrprg.c
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/* bam_addrprg.c -- samtools command to add or replace readgroups.
Copyright (c) 2013, 2015, 2016 Genome Research Limited.
Copyright (c) 2013, 2015-2017, 2019 Genome Research Limited.
Author: Martin O. Pollard <[email protected]>
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2 changes: 1 addition & 1 deletion bam_aux.c
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/* bam_aux.c -- remaining aux field handling.
Copyright (C) 2008-2010, 2013 Genome Research Ltd.
Copyright (C) 2008-2010, 2013, 2015, 2019 Genome Research Ltd.
Portions copyright (C) 2011 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_cat.c
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/* bam_cat.c -- efficiently concatenates bam files.
Copyright (C) 2008-2009, 2011-2013, 2015-2016 Genome Research Ltd.
Copyright (C) 2008-2009, 2011-2013, 2015-2017, 2019 Genome Research Ltd.
Modified SAMtools work copyright (C) 2010 Illumina, Inc.
Permission is hereby granted, free of charge, to any person obtaining a copy
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2 changes: 1 addition & 1 deletion bam_fastq.c
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/* bam_fastq.c -- FASTA and FASTQ file generation
Copyright (C) 2009-2017 Genome Research Ltd.
Copyright (C) 2009-2017, 2019 Genome Research Ltd.
Portions copyright (C) 2009, 2011, 2012 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_index.c
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/* bam_index.c -- index and idxstats subcommands.
Copyright (C) 2008-2011, 2013, 2014 Genome Research Ltd.
Copyright (C) 2008-2011, 2013-2016, 2018, 2019 Genome Research Ltd.
Portions copyright (C) 2010 Broad Institute.
Portions copyright (C) 2013 Peter Cock, The James Hutton Institute.
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2 changes: 1 addition & 1 deletion bam_markdup.c
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/* bam_markdup.c -- Mark duplicates from a coord sorted file that has gone
through fixmates with the mate scoring option on.
Copyright (C) 2017-19 Genome Research Ltd.
Copyright (C) 2017-2019 Genome Research Ltd.
Author: Andrew Whitwham <[email protected]>
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2 changes: 1 addition & 1 deletion bam_quickcheck.c
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/* bam_quickcheck.c -- quickcheck subcommand.
Copyright (C) 2015 Genome Research Ltd.
Copyright (C) 2015-2017 Genome Research Ltd.
Author: Joshua C. Randall <[email protected]>
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2 changes: 1 addition & 1 deletion bam_rmdup.c
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/* bam_rmdup.c -- duplicate read detection.
Copyright (C) 2009, 2015 Genome Research Ltd.
Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
Portions copyright (C) 2009 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_rmdupse.c
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/* bam_rmdupse.c -- duplicate read detection for unpaired reads.
Copyright (C) 2009, 2015 Genome Research Ltd.
Copyright (C) 2009, 2015, 2016, 2019 Genome Research Ltd.
Portions copyright (C) 2009 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_sort.c
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/* bam_sort.c -- sorting and merging.
Copyright (C) 2008-2016 Genome Research Ltd.
Copyright (C) 2008-2019 Genome Research Ltd.
Portions copyright (C) 2009-2012 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_split.c
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/* bam_split.c -- split subcommand.
Copyright (C) 2013-2016,2018 Genome Research Ltd.
Copyright (C) 2013-2016,2018-2019 Genome Research Ltd.
Author: Martin Pollard <[email protected]>
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2 changes: 1 addition & 1 deletion bam_stat.c
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/* bam_stat.c -- flagstat subcommand.
Copyright (C) 2009, 2011, 2013-2015 Genome Research Ltd.
Copyright (C) 2009, 2011, 2013-2015, 2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_tview.c
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/* bam_tview.c -- tview subcommand.
Copyright (C) 2008-2016 Genome Research Ltd.
Copyright (C) 2008-2016, 2019 Genome Research Ltd.
Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_tview.h
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/* bam_tview.h -- tview subcommand.
Copyright (C) 2008, 2013 Genome Research Ltd.
Copyright (C) 2008, 2013, 2019 Genome Research Ltd.
Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bam_tview_curses.c
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/* bam_tview_curses.c -- curses tview implementation.
Copyright (C) 2008-2013 Genome Research Ltd.
Copyright (C) 2008-2015, 2019 Genome Research Ltd.
Portions copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Author: Heng Li <[email protected]>
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1 change: 1 addition & 0 deletions bam_tview_html.c
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/* bam_tview_html.c -- HTML tview output.
Copyright (C) 2013 Pierre Lindenbaum, Institut du Thorax, INSERM U1087, Université de Nantes.
Copyright (C) 2019 Genome Research Ltd.
Author: Pierre Lindenbaum <[email protected]>
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2 changes: 1 addition & 1 deletion bamshuf.c
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/* bamshuf.c -- collate subcommand.
Copyright (C) 2012 Broad Institute.
Copyright (C) 2013, 2015, 2018 Genome Research Ltd.
Copyright (C) 2013, 2015-2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bedcov.c
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/* bedcov.c -- bedcov subcommand.
Copyright (C) 2012 Broad Institute.
Copyright (C) 2013-2014 Genome Research Ltd.
Copyright (C) 2013-2014, 2018, 2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion bedidx.c
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/* bedidx.c -- BED file indexing.
Copyright (C) 2011 Broad Institute.
Copyright (C) 2014,2017 Genome Research Ltd.
Copyright (C) 2014, 2017-2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion configure.ac
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# Configure script for samtools, utilities for Sequence Alignment/Map files.
#
# Copyright (C) 2015 Genome Research Ltd.
# Copyright (C) 2015, 2017 Genome Research Ltd.
#
# Author: John Marshall <[email protected]>
#
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2 changes: 1 addition & 1 deletion doc/samtools-depth.1
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.SH NAME
samtools depth \- computes the read depth at each position or region
.\"
.\" 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 <[email protected]>
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2 changes: 1 addition & 1 deletion doc/samtools-fasta.1
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.SH NAME
samtools fasta / fastq \- converts a SAM/BAM/CRAM file to FASTA or FASTQ
.\"
.\" 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 <[email protected]>
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2 changes: 1 addition & 1 deletion doc/samtools-flagstat.1
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.SH NAME
samtools flagstat \- counts the number of alignments for each FLAG type
.\"
.\" 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 <[email protected]>
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2 changes: 1 addition & 1 deletion doc/samtools-mpileup.1
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.SH NAME
samtools mpileup \- produces "pileup" textual format from an alignment
.\"
.\" 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 <[email protected]>
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2 changes: 1 addition & 1 deletion doc/samtools-reheader.1
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.SH NAME
samtools reheader \- replaces the header in the input file
.\"
.\" 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 <[email protected]>
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2 changes: 1 addition & 1 deletion doc/samtools-tview.1
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.SH NAME
samtools tview \- display alignments in a curses-based interactive viewer.
.\"
.\" 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 <[email protected]>
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2 changes: 1 addition & 1 deletion doc/samtools-view.1
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.SH NAME
samtools view \- views and converts 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 <[email protected]>
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2 changes: 1 addition & 1 deletion doc/samtools.1
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.SH NAME
samtools \- Utilities for the Sequence Alignment/Map (SAM) format
.\"
.\" 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 <[email protected]>
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2 changes: 1 addition & 1 deletion misc/novo2sam.pl
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#
# Author : Heng Li <[email protected]>
#
# Copyright (C) 2009,2014 Genome Research Ltd.
# Copyright (C) 2009,2014, 2019 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
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2 changes: 1 addition & 1 deletion phase.c
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/* phase.c -- phase subcommand.
Copyright (C) 2011 Broad Institute.
Copyright (C) 2013-2016 Genome Research Ltd.
Copyright (C) 2013-2016, 2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion sam.c
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/* sam.c -- format-neutral SAM/BAM API.
Copyright (C) 2009, 2012-2015 Genome Research Ltd.
Copyright (C) 2009, 2012-2016 Genome Research Ltd.
Portions copyright (C) 2011 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion sam.h
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/* sam.h -- format-neutral SAM/BAM API.
Copyright (C) 2009, 2013-2015 Genome Research Ltd.
Copyright (C) 2009, 2013-2015, 2019 Genome Research Ltd.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion sam_opts.c
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/* sam_opts.c -- utilities to aid parsing common command line options.
Copyright (C) 2015 Genome Research Ltd.
Copyright (C) 2015, 2019 Genome Research Ltd.
Author: James Bonfield <[email protected]>
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2 changes: 1 addition & 1 deletion sam_opts.h
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/* sam_opts.h -- utilities to aid parsing common command line options.
Copyright (C) 2015 Genome Research Ltd.
Copyright (C) 2015, 2019 Genome Research Ltd.
Author: James Bonfield <[email protected]>
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2 changes: 1 addition & 1 deletion sam_utils.c
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/* sam_utils.c -- various utilities internal to samtools.
Copyright (C) 2014-2016 Genome Research Ltd.
Copyright (C) 2014-2016, 2018, 2019 Genome Research Ltd.
Author: John Marshall <[email protected]>
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2 changes: 1 addition & 1 deletion sam_view.c
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/* sam_view.c -- SAM<->BAM<->CRAM conversion.
Copyright (C) 2009-2017 Genome Research Ltd.
Copyright (C) 2009-2019 Genome Research Ltd.
Portions copyright (C) 2009, 2011, 2012 Broad Institute.
Author: Heng Li <[email protected]>
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2 changes: 1 addition & 1 deletion samtools.h
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/* samtools.h -- utility routines.
Copyright (C) 2013-2015 Genome Research Ltd.
Copyright (C) 2013-2015, 2019 Genome Research Ltd.
Author: Petr Danecek <[email protected]>
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2 changes: 1 addition & 1 deletion stats_isize.c
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/* stats_isize.c -- generalised insert size calculation for samtools stats.
Copyright (C) 2014 Genome Research Ltd.
Copyright (C) 2014, 2018 Genome Research Ltd.
Author: Nicholas Clarke <[email protected]>
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2 changes: 1 addition & 1 deletion test/maintainer/check_copyright.pl
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#
# Author : Rob Davies <[email protected]>
#
# Copyright (C) 2018 Genome Research Ltd.
# Copyright (C) 2018-2019 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
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2 changes: 1 addition & 1 deletion test/maintainer/check_spaces.pl
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#
# Author : Rob Davies <[email protected]>
#
# Copyright (C) 2018 Genome Research Ltd.
# Copyright (C) 2018-2019 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
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2 changes: 1 addition & 1 deletion test/merge/test_trans_tbl_init.c
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/* test/merge/test_trans_tbl_init.c -- merge test harness.
Copyright (C) 2013, 2014 Genome Research Ltd.
Copyright (C) 2013-2016, 2019 Genome Research Ltd.
Author: Martin O. Pollard <[email protected]>
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2 changes: 1 addition & 1 deletion test/split/test_count_rg.c
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/* test/split/test_count_rg.c -- split test cases.
Copyright (C) 2014 Genome Research Ltd.
Copyright (C) 2014, 2019 Genome Research Ltd.
Author: Martin O. Pollard <[email protected]>
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