Skip to content

Commit

Permalink
Changed version info for minor release
Browse files Browse the repository at this point in the history
  • Loading branch information
FelixKrueger committed Jul 26, 2021
1 parent 5679802 commit 73844f4
Show file tree
Hide file tree
Showing 12 changed files with 21 additions and 21 deletions.
4 changes: 2 additions & 2 deletions NOMe_filtering
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use Getopt::Long;
use Cwd;
use Carp;

## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
## This program is Copyright (C) 2010-21, 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
Expand All @@ -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 = 'v0.23.0';
my $nome_version = 'v0.23.1';

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();

Expand Down
4 changes: 2 additions & 2 deletions bam2nuc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use Getopt::Long;
use Cwd;
use Carp;

## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
## This program is Copyright (C) 2010-21, 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
Expand All @@ -31,7 +31,7 @@ my %freqs; # keeping a record of which chromosomes have been processed
my %genomic_freqs;
my %processed;

my $bam2nuc_version = 'v0.23.0';
my $bam2nuc_version = 'v0.23.1';

my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline();

Expand Down
4 changes: 2 additions & 2 deletions bismark
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ use Getopt::Long;
use FindBin qw($RealBin);
use lib "$RealBin/../lib";

## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
## This program is Copyright (C) 2010-21, 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
Expand All @@ -25,7 +25,7 @@ use lib "$RealBin/../lib";


my $parent_dir = getcwd();
my $bismark_version = 'v0.23.0';
my $bismark_version = 'v0.23.1';
my $start_run = time();
my $command_line = join (" ",@ARGV);

Expand Down
4 changes: 2 additions & 2 deletions bismark2bedGraph
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use Getopt::Long;
use Cwd;
use Carp;

## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
## This program is Copyright (C) 2010-21, 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
Expand All @@ -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 = 'v0.23.0';
my $bismark2bedGraph_version = 'v0.23.1';

my @bedfiles;
my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total
Expand Down
4 changes: 2 additions & 2 deletions bismark2report
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ use Getopt::Long;
use FindBin qw($RealBin);
use lib "$RealBin/../lib";

## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
## This program is Copyright (C) 2010-21, 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
Expand All @@ -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 = 'v0.23.0';
my $bismark2report_version = 'v0.23.1';
my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);

my ($output_dir,$verbose,$manual_output_file) = process_commandline();
Expand Down
4 changes: 2 additions & 2 deletions bismark2summary
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ use Getopt::Long;
use FindBin qw($RealBin);
use lib "$RealBin/../lib";

## This program is Copyright (C) 2010-20, Felix Krueger <[email protected]>.
## This program is Copyright (C) 2010-21, Felix Krueger <[email protected]>.
## Thanks to Phil Ewels <[email protected]> (who wrote a first version of this
## script in 2013 or so when it was still 'legal' to use Highcharts.js (or maybe it
## never was?....))
Expand All @@ -22,7 +22,7 @@ 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 $bismark_version = '0.22.4';
my $bismark_version = '0.23.1';

# Last modified 09 11 2020

Expand Down
2 changes: 1 addition & 1 deletion bismark_genome_preparation
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ my $genomic_composition;
my %genomic_freqs; # storing the genomic sequence composition
my %freqs;

my $bismark_version = 'v0.23.0dev';
my $bismark_version = 'v0.23.1';
my $last_modified = "27 Jan 2021";

my $command_line = GetOptions ('verbose' => \$verbose,
Expand Down
4 changes: 2 additions & 2 deletions bismark_methylation_extractor
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ use Carp;
use FindBin qw($RealBin);
use lib "$RealBin/../lib";

## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
## This program is Copyright (C) 2010-21, 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
Expand All @@ -29,7 +29,7 @@ my $parent_dir = getcwd();

my %fhs;

my $version = 'v0.23.0';
my $version = 'v0.23.1';
my ($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
Expand Down
4 changes: 2 additions & 2 deletions coverage2cytosine
View file
Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use Getopt::Long;
use Cwd;
use Carp;

## This program is Copyright (C) 2010-20, Felix Krueger ([email protected])
## This program is Copyright (C) 2010-21, 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
Expand All @@ -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 = 'v0.23.0';
my $coverage2cytosine_version = 'v0.23.1';

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();

Expand Down
2 changes: 1 addition & 1 deletion deduplicate_bismark
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 = 'v0.23.0';
my $dedup_version = 'v0.23.1';
my @filenames;

my ($single,$paired,$global_single,$global_paired,$samtools_path,$bam,$rrbs,$multiple,$output_dir,$outfile,$parallel) = process_commandline();
Expand Down
2 changes: 1 addition & 1 deletion filter_non_conversion
View file
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ $|++;
## along with this program. If not, see <http://www.gnu.org/licenses/>.

my $parent_dir = getcwd();
my $filter_version = 'v0.23.0dev';
my $filter_version = 'v0.23.1';

my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive,$percentage_cutoff,$minimum_count) = process_commandline();

Expand Down
4 changes: 2 additions & 2 deletions methylation_consistency
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ use warnings;
use strict;
use Getopt::Long;

my $VERSION = "0.23.0dev";
my $VERSION = "0.23.1";
my ($min_count,$global_single,$global_paired,$lower_threshold,$upper_threshold,$samtools_path) = process_commandline();


Expand Down Expand Up @@ -39,7 +39,7 @@ sub process_commandline{
Bismark Read Methylation Constistency
v$VERSION
Copyright 2019-20 Felix Krueger, Babraham Bioinformatics
Copyright 2019-21 Felix Krueger, Babraham Bioinformatics
www.bioinformatics.babraham.ac.uk/projects/bismark/
https://github.com/FelixKrueger/Bismark
Expand Down

0 comments on commit 73844f4

Please sign in to comment.