From e3fec9dfb4acb013ee5b25623684e890ff46ab08 Mon Sep 17 00:00:00 2001 From: Felix Krueger Date: Wed, 27 Sep 2023 09:01:50 +0100 Subject: [PATCH] Preparing release --- NOMe_filtering | 2 +- bam2nuc | 2 +- bismark | 2 +- bismark2bedGraph | 2 +- bismark2report | 2 +- bismark2summary | 2 +- bismark_genome_preparation | 2 +- bismark_methylation_extractor | 2 +- coverage2cytosine | 2 +- deduplicate_bismark | 2 +- filter_non_conversion | 2 +- merge_coverage_files_ARGV.py | 2 -- methylation_consistency | 2 +- 13 files changed, 12 insertions(+), 14 deletions(-) diff --git a/NOMe_filtering b/NOMe_filtering index 4010f3d..0fc326e 100755 --- 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 index 986feaf..6490893 100755 --- 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 index 095634f..b3e574d 100755 --- 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 index 2dcec77..a7872b9 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 = 'v0.24.1'; +my $bismark2bedGraph_version = 'v0.24.2'; my @bedfiles; my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total diff --git a/bismark2report b/bismark2report index a94e8ac..3ce2a03 100755 --- a/bismark2report +++ b/bismark2report @@ -20,7 +20,7 @@ use lib "$RealBin/../lib"; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -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 index f0dbe5d..dd2cfd3 100755 --- 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 . -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 index 2857e50..b504938 100755 --- 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 index b9ed086..1139157 100755 --- 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 index 9481cbe..e8d531a 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 = 'v0.24.1dev'; +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 index 08c4ca7..850eaeb 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 = 'v0.24.1'; +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 index ba5dabf..73d1f98 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 = 'v0.24.1'; +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 index c19dffc..2accaa4 100755 --- 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 index e3bc08a..60fdff7 100755 --- 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){