Preparing release

FelixKrueger · Sep 27, 2023 · e3fec9d · e3fec9d
1 parent 5e970a7
commit e3fec9d
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Showing 13 changed files with 12 additions and 14 deletions.
diff --git a/NOMe_filtering b/NOMe_filtering
@@ -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 = 'v0.24.1';
+my $nome_version = 'v0.24.2';
 
 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
@@ -31,7 +31,7 @@ my %freqs;   # keeping a record of which chromosomes have been processed
 my %genomic_freqs;
 my %processed;
 
-my $bam2nuc_version = 'v0.24.1';
+my $bam2nuc_version = 'v0.24.2';
 
 my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline();
 

diff --git a/bismark b/bismark
@@ -25,7 +25,7 @@ use lib "$RealBin/../lib";
 
 my $parent_dir = getcwd();
 
-my $bismark_version = 'v0.24.1dev';
+my $bismark_version = 'v0.24.2';
 my $copyright_dates = "2010-23";
 
 my $start_run = time();

diff --git 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 <http://www.gnu.org/licenses/>.
 
-my $bismark2bedGraph_version = 'v0.24.1';
+my $bismark2bedGraph_version = 'v0.24.2';
 
 my @bedfiles;
 my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total

diff --git a/bismark2report b/bismark2report
@@ -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 = 'v0.24.1';
+my $bismark2report_version = 'v0.24.2';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();

diff --git a/bismark2summary b/bismark2summary
@@ -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 = '0.24.1';
+my $bismark_version = '0.24.2';
 
 # Last modified 09 11 2020
 

diff --git a/bismark_genome_preparation b/bismark_genome_preparation
@@ -42,7 +42,7 @@ my %genomic_freqs; # storing the genomic sequence composition
 my %freqs;
 
 
-my $bismark_version = 'v0.24.1';
+my $bismark_version = 'v0.24.2';
 my $copyright_date = '2010-23';
 my $last_modified = "19 May 2022";
 

diff --git a/bismark_methylation_extractor b/bismark_methylation_extractor
@@ -29,7 +29,7 @@ my $parent_dir = getcwd();
 
 my %fhs;
 
-my $version = 'v0.24.1';
+my $version = 'v0.24.2';
 my ($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
@@ -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 = 'v0.24.1dev';
+my $coverage2cytosine_version = 'v0.24.2';
 
 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
@@ -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 = 'v0.24.1';
+my $dedup_version = 'v0.24.2';
 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
@@ -22,7 +22,7 @@ $|++;
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 my $parent_dir = getcwd();
-my $filter_version = 'v0.24.1';
+my $filter_version = 'v0.24.2';
 
 my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive,$percentage_cutoff,$minimum_count) = process_commandline();
 

diff --git a/merge_coverage_files_ARGV.py b/merge_coverage_files_ARGV.py
@@ -14,8 +14,6 @@
 #         print_options(options)
 
 
-
-
 def parse_options():
     parser = argparse.ArgumentParser(description="Set base-name to write merged Bismark coverage files to")
     parser.add_argument("-b","--basename", type=str, help="Basename of file to write merged coverage output to (default 'merged_coverage_file')", default="merged_coverage_file.cov.gz")

diff --git a/methylation_consistency b/methylation_consistency
@@ -3,7 +3,7 @@ use warnings;
 use strict;
 use Getopt::Long;
 
-my $VERSION = "0.24.1";
+my $VERSION = "0.24.2";
 my ($min_count,$global_single,$global_paired,$lower_threshold,$upper_threshold,$samtools_path,$chh) = process_commandline();
 
 if ($chh){