Preparing version numbers for 0.23.0 release

NOMe_filtering

@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-19, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
 
 ## 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();
 

bam2nuc

@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-19, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
 
 ## 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
 	       

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 ([email protected])
+## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
 
 ## 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);
 

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 <http://www.gnu.org/licenses/>.
 
-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

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 ([email protected])
+## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
 
 ## 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 <http://www.gnu.org/licenses/>.
 
-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();

bismark_genome_preparation

@@ -6,7 +6,7 @@ use Getopt::Long;
 $|++;
 
 
-## This program is Copyright (C) 2010-19, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
 
 ## 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,

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

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();
 

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();

filter_non_conversion

@@ -22,7 +22,7 @@ $|++;
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 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();
 

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();