Update copyright dates to 2020 where needed.

With some exclusions for minor changes.
valeriuo · Aug 4, 2020 · 6383daa · 6383daa
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diff --git 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 <[email protected]>

diff --git 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 <[email protected]>
 

diff --git 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 <[email protected]>
 

diff --git 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 <[email protected]>
 

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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
@@ -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 <[email protected]>
 #

diff --git 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 <[email protected]>
 

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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
@@ -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 <[email protected]>
 

diff --git 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 <[email protected]>
 

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>

diff --git 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 <[email protected]>
 

diff --git 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 <[email protected]>
 #

diff --git 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 <[email protected]>
 

diff --git 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 <[email protected]>
 

diff --git 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
@@ -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 <[email protected]>