diff --git a/NOMe_filtering b/NOMe_filtering index a8faa4c..969d097 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 = 'v0.22.2'; +my $nome_version = 'v0.22.3'; my ($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 a71df89..66f0868 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 = 'v0.22.2'; +my $bam2nuc_version = 'v0.22.3'; my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline(); diff --git a/bismark b/bismark index a5cdb54..7e0c834 100755 --- a/bismark +++ b/bismark @@ -25,7 +25,7 @@ use lib "$RealBin/../lib"; my $parent_dir = getcwd(); -my $bismark_version = 'v0.22.2'; +my $bismark_version = 'v0.22.3'; my $start_run = time(); my $command_line = join (" ",@ARGV); diff --git a/bismark2bedGraph b/bismark2bedGraph index af1acd8..d78c728 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 = 'v0.22.2'; +my $bismark2bedGraph_version = 'v0.22.3'; my @bedfiles; my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total diff --git a/bismark2report b/bismark2report index 65f2432..dbeb896 100755 --- a/bismark2report +++ b/bismark2report @@ -20,7 +20,7 @@ use lib "$RealBin/../lib"; ## You should have received a copy of the GNU General Public License ## along with this program. If not, see . -my $bismark2report_version = 'v0.22.2'; +my $bismark2report_version = 'v0.22.3'; my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports); my ($output_dir,$verbose,$manual_output_file) = process_commandline(); diff --git a/bismark2summary b/bismark2summary index 65ad43d..ec5d195 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 = '0.22.2'; +my $bismark_version = '0.22.3'; # Last modified 31 07 2019 diff --git a/bismark_genome_preparation b/bismark_genome_preparation index ebf16ab..807cd7c 100755 --- a/bismark_genome_preparation +++ b/bismark_genome_preparation @@ -40,7 +40,7 @@ my $genomic_composition; my %genomic_freqs; # storing the genomic sequence composition my %freqs; -my $bismark_version = 'v0.22.2'; +my $bismark_version = 'v0.22.3'; my $last_modified = "14 April 2019"; my $command_line = GetOptions ('verbose' => \$verbose, diff --git a/bismark_methylation_extractor b/bismark_methylation_extractor index 409cfa9..1df0b6b 100755 --- a/bismark_methylation_extractor +++ b/bismark_methylation_extractor @@ -29,7 +29,7 @@ my $parent_dir = getcwd(); my %fhs; -my $version = 'v0.22.2'; +my $version = 'v0.22.3'; my ($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) = process_commandline(); ### only needed for bedGraph output diff --git a/coverage2cytosine b/coverage2cytosine index f386026..aa79321 100755 --- a/coverage2cytosine +++ b/coverage2cytosine @@ -22,7 +22,7 @@ use Carp; my %chromosomes; # storing sequence information of all chromosomes/scaffolds my %processed; # keeping a record of which chromosomes have been processed -my $coverage2cytosine_version = 'v0.22.2'; +my $coverage2cytosine_version = 'v0.22.3'; my ($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) = process_commandline(); diff --git a/deduplicate_bismark b/deduplicate_bismark index e4a029b..03b3683 100755 --- a/deduplicate_bismark +++ b/deduplicate_bismark @@ -47,7 +47,7 @@ use Cwd; ### 26 03 2019 ### Adapting to also work with softclipped reads (CIGAR operation S) -my $dedup_version = 'v0.22.2'; +my $dedup_version = 'v0.22.3'; my @filenames; my ($single,$paired,$global_single,$global_paired,$samtools_path,$bam,$rrbs,$multiple,$output_dir,$outfile) = process_commandline(); diff --git a/filter_non_conversion b/filter_non_conversion index d062438..bc5dcad 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 = 'v0.22.2'; +my $filter_version = 'v0.22.3'; my ($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 1b3e387..4b0a005 100755 --- a/methylation_consistency +++ b/methylation_consistency @@ -3,7 +3,7 @@ use warnings; use strict; use Getopt::Long; -my $VERSION = "0.22.2_dev"; +my $VERSION = "0.22.3"; my ($min_count,$global_single,$global_paired,$lower_threshold,$upper_threshold,$samtools_path) = process_commandline();