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Updated copyright and bowtie2 version recommendation language
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jeffreybarrick committed May 18, 2022
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5 changes: 2 additions & 3 deletions ChangeLog
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Version 0.37.0
* Warn or error when bowtie2 versions that give inconsistent or problematic
output are used. Update conda recipe to install the recommended bowtie2
version 2.2.4 to try to enforce consistency.
* Warns that breseq results can vary (usually only slightly) with different
bowtie2 versions and recommends a specific version for consistency.
* Added back code for shifting indels to improve mutation calling.
* Added an option for gdtools APPLY to output a new GD file showing the
positions of each mutation in the (mutated) output genome.
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2 changes: 1 addition & 1 deletion src/c/breseq/alignment.cpp
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LICENSE AND COPYRIGHT
Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin
breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/alignment_output.cpp
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* LICENSE AND COPYRIGHT
*
* Copyright (c) 2008-2010 Michigan State University
* Copyright (c) 2011-2017 The University of Texas at Austin
* Copyright (c) 2011-2022 The University of Texas at Austin
*
* breseq is free software; you can redistribute it and/or modify it under the
* terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/breseq_cmdline.cpp
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LICENSE AND COPYRIGHT
Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin
breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/calculate_trims.cpp
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LICENSE AND COPYRIGHT
Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin
breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/candidate_junctions.cpp
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LICENSE AND COPYRIGHT
Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin
breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/contingency_loci.cpp
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LICENSE AND COPYRIGHT
Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin
breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/coverage_distribution.cpp
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LICENSE AND COPYRIGHT
Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin
breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/coverage_distribution.r
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## LICENSE AND COPYRIGHT
##
## Copyright (c) 2008-2010 Michigan State University
## Copyright (c) 2011-2017 The University of Texas at Austin
## Copyright (c) 2011-2022 The University of Texas at Austin
##
## breseq is free software; you can redistribute it and/or modify it under the
## terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/coverage_output.cpp
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* LICENSE AND COPYRIGHT
*
* Copyright (c) 2008-2010 Michigan State University
* Copyright (c) 2011-2017 The University of Texas at Austin
* Copyright (c) 2011-2022 The University of Texas at Austin
*
* breseq is free software; you can redistribute it and/or modify it under the
* terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/error_count.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/fasta.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/fastq.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/flagged_regions.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/gdtools_cmdline.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/genome_diff.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/genome_diff_entry.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/identify_mutations.cpp
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/alignment.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/alignment_output.h
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* LICENSE AND COPYRIGHT
*
* Copyright (c) 2008-2010 Michigan State University
* Copyright (c) 2011-2017 The University of Texas at Austin
* Copyright (c) 2011-2022 The University of Texas at Austin
*
* breseq is free software; you can redistribute it and/or modify it under the
* terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/calculate_trims.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/candidate_junctions.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/common.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/contingency_loci.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/counted_ptr.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/coverage_distribution.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/coverage_output.h
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* LICENSE AND COPYRIGHT
*
* Copyright (c) 2008-2010 Michigan State University
* Copyright (c) 2011-2017 The University of Texas at Austin
* Copyright (c) 2011-2022 The University of Texas at Austin
*
* breseq is free software; you can redistribute it and/or modify it under the
* terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/error_count.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/fasta.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/fastq.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/file_parse_errors.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/flagged_regions.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/genome_diff.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/genome_diff_entry.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/identify_mutations.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/mutation_predictor.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/output.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/pileup.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/pileup_base.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/reference_sequence.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/resolve_alignments.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/samtools_commands.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/settings.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
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2 changes: 1 addition & 1 deletion src/c/breseq/libbreseq/storable.h
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LICENSE AND COPYRIGHT

Copyright (c) 2008-2010 Michigan State University
Copyright (c) 2011-2017 The University of Texas at Austin
Copyright (c) 2011-2022 The University of Texas at Austin

breseq is free software; you can redistribute it and/or modify it under the
terms the GNU General Public License as published by the Free Software
Expand Down
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