From 87df331afa21772faa97c435d69f49b5822a7060 Mon Sep 17 00:00:00 2001 From: FelixKrueger Date: Mon, 9 Nov 2020 13:13:15 +0000 Subject: [PATCH] Preparing version numbers for 0.23.0 release --- NOMe_filtering | 4 ++-- bam2nuc | 6 +++--- bismark | 4 ++-- bismark2bedGraph | 2 +- bismark2report | 4 ++-- bismark_genome_preparation | 4 ++-- bismark_methylation_extractor | 2 +- coverage2cytosine | 2 +- deduplicate_bismark | 2 +- filter_non_conversion | 2 +- methylation_consistency | 2 +- 11 files changed, 17 insertions(+), 17 deletions(-) diff --git a/NOMe_filtering b/NOMe_filtering index 969d097..8e77804 100755 --- a/NOMe_filtering +++ b/NOMe_filtering @@ -6,7 +6,7 @@ use Getopt::Long; use Cwd; use Carp; -## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-20, Felix Krueger (felix.krueger@babraham.ac.uk) ## This program is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by @@ -23,7 +23,7 @@ use Carp; my %chromosomes; # storing sequence information of all chromosomes/scaffolds my %processed; # keeping a record of which chromosomes have been processed -my $nome_version = 'v0.22.3'; +my $nome_version = 'v0.23.0'; my ($output_dir,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$parent_dir,$coverage_infile,$cytosine_out,$merge_CpGs,$gc_context,$gzip,$nome) = process_commandline(); diff --git a/bam2nuc b/bam2nuc index 66f0868..df35d0b 100755 --- a/bam2nuc +++ b/bam2nuc @@ -6,7 +6,7 @@ use Getopt::Long; use Cwd; use Carp; -## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-20, Felix Krueger (felix.krueger@babraham.ac.uk) ## This program is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by @@ -31,7 +31,7 @@ my %freqs; # keeping a record of which chromosomes have been processed my %genomic_freqs; my %processed; -my $bam2nuc_version = 'v0.22.3'; +my $bam2nuc_version = 'v0.23.0'; my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline(); @@ -380,7 +380,7 @@ sub process_commandline{ bam2nuc Bismark Version: $bam2nuc_version - Copyright 2010-19 Felix Krueger, Babraham Bioinformatics + Copyright 2010-20 Felix Krueger, Babraham Bioinformatics www.bioinformatics.babraham.ac.uk/projects/bismark/ https://github.com/FelixKrueger/Bismark diff --git a/bismark b/bismark index 7e0c834..f65ba07 100755 --- a/bismark +++ b/bismark @@ -8,7 +8,7 @@ use Getopt::Long; use FindBin qw($RealBin); use lib "$RealBin/../lib"; -## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-20, Felix Krueger (felix.krueger@babraham.ac.uk) ## This program is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ use lib "$RealBin/../lib"; my $parent_dir = getcwd(); -my $bismark_version = 'v0.22.3'; +my $bismark_version = 'v0.23.0'; my $start_run = time(); my $command_line = join (" ",@ARGV); diff --git a/bismark2bedGraph b/bismark2bedGraph index 0fd13a7..13084a2 100755 --- a/bismark2bedGraph +++ b/bismark2bedGraph @@ -21,7 +21,7 @@ use Carp; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -my $bismark2bedGraph_version = 'v0.22.3dev'; +my $bismark2bedGraph_version = 'v0.23.0'; my @bedfiles; my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total diff --git a/bismark2report b/bismark2report index dbeb896..c02c425 100755 --- a/bismark2report +++ b/bismark2report @@ -5,7 +5,7 @@ use Getopt::Long; use FindBin qw($RealBin); use lib "$RealBin/../lib"; -## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-20, Felix Krueger (felix.krueger@babraham.ac.uk) ## This program is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by @@ -20,7 +20,7 @@ use lib "$RealBin/../lib"; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -my $bismark2report_version = 'v0.22.3'; +my $bismark2report_version = 'v0.23.0'; my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports); my ($output_dir,$verbose,$manual_output_file) = process_commandline(); diff --git a/bismark_genome_preparation b/bismark_genome_preparation index 807cd7c..5cc968b 100755 --- a/bismark_genome_preparation +++ b/bismark_genome_preparation @@ -6,7 +6,7 @@ use Getopt::Long; $|++; -## This program is Copyright (C) 2010-19, Felix Krueger (felix.krueger@babraham.ac.uk) +## This program is Copyright (C) 2010-20, Felix Krueger (felix.krueger@babraham.ac.uk) ## This program is free software: you can redistribute it and/or modify ## it under the terms of the GNU General Public License as published by @@ -40,7 +40,7 @@ my $genomic_composition; my %genomic_freqs; # storing the genomic sequence composition my %freqs; -my $bismark_version = 'v0.22.3'; +my $bismark_version = 'v0.23.0'; my $last_modified = "14 April 2019"; my $command_line = GetOptions ('verbose' => \$verbose, diff --git a/bismark_methylation_extractor b/bismark_methylation_extractor index 699af9c..fc73bce 100755 --- a/bismark_methylation_extractor +++ b/bismark_methylation_extractor @@ -29,7 +29,7 @@ my $parent_dir = getcwd(); my %fhs; -my $version = 'v0.22.3dev'; +my $version = 'v0.23.0'; my ($ignore,$genomic_fasta,$single,$paired,$full,$report,$no_overlap,$merge_non_CpG,$output_dir,$no_header,$bedGraph,$remove,$coverage_threshold,$counts,$cytosine_report,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$sort_size,$samtools_path,$gzip,$ignore_r2,$mbias_off,$mbias_only,$gazillion,$ample_mem,$ignore_3prime,$ignore_3prime_r2,$multicore,$yacht,$ucsc) = process_commandline(); ### only needed for bedGraph output diff --git a/coverage2cytosine b/coverage2cytosine index 285e45d..b6ddca8 100755 --- a/coverage2cytosine +++ b/coverage2cytosine @@ -23,7 +23,7 @@ use Carp; my %chromosomes; # storing sequence information of all chromosomes/scaffolds my %processed; # keeping a record of which chromosomes have been processed my %context_summary; # storing methylation values for all contexts for NOMe-seq or scNMT-experiments -my $coverage2cytosine_version = 'v0.22.3dev'; +my $coverage2cytosine_version = 'v0.23.0'; my ($output_dir,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$parent_dir,$coverage_infile,$cytosine_out,$merge_CpGs,$gc_context,$gzip,$tetra,$nome,$disco,$threshold,$drach) = process_commandline(); diff --git a/deduplicate_bismark b/deduplicate_bismark index 6b97a4d..6dc6b33 100755 --- a/deduplicate_bismark +++ b/deduplicate_bismark @@ -7,7 +7,7 @@ use Cwd; ### This script is supposed to remove alignments to the same position in the genome which can arise by e.g. PCR amplification ### Paired-end alignments are considered a duplicate if both partner reads start and end at the exact same position -my $dedup_version = 'v0.22.3_dev'; +my $dedup_version = 'v0.23.0'; my @filenames; my ($single,$paired,$global_single,$global_paired,$samtools_path,$bam,$rrbs,$multiple,$output_dir,$outfile,$parallel) = process_commandline(); diff --git a/filter_non_conversion b/filter_non_conversion index bc5dcad..b570d4b 100755 --- a/filter_non_conversion +++ b/filter_non_conversion @@ -22,7 +22,7 @@ $|++; ## along with this program. If not, see . my $parent_dir = getcwd(); -my $filter_version = 'v0.22.3'; +my $filter_version = 'v0.23.0'; my ($single,$paired); my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive,$percentage_cutoff,$minimum_count) = process_commandline(); diff --git a/methylation_consistency b/methylation_consistency index 9420909..1a9044c 100755 --- a/methylation_consistency +++ b/methylation_consistency @@ -3,7 +3,7 @@ use warnings; use strict; use Getopt::Long; -my $VERSION = "0.22.3dev"; +my $VERSION = "0.23.0"; my ($min_count,$global_single,$global_paired,$lower_threshold,$upper_threshold,$samtools_path) = process_commandline();