Peparing for Easter release (local mode)

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 = 'v0.21.0';
+my $nome_version = 'v0.22.0';
 
 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

@@ -31,7 +31,7 @@ my %freqs;   # keeping a record of which chromosomes have been processed
 my %genomic_freqs;
 my %processed;
 
-my $bam2nuc_version = 'v0.21.0_dev';
+my $bam2nuc_version = 'v0.22.0';
 
 my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline();
 

bismark

@@ -25,7 +25,7 @@ use lib "$RealBin/../lib";
 
 
 my $parent_dir = getcwd();
-my $bismark_version = 'v0.21.0_dev';
+my $bismark_version = 'v0.22.0';
 my $start_run = time();
 # warn "Run started at: $start_run\n";
 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 = 'v0.21.0';
+my $bismark2bedGraph_version = 'v0.22.0';
 
 my @bedfiles;
 my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total

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 = 'v0.21.0';
+my $bismark2report_version = 'v0.22.0';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();

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 = '0.21.0';
+my $bismark_version = '0.22.0';
 
 # Last modified 14 02 2019
 

bismark_genome_preparation

@@ -40,7 +40,7 @@ my $genomic_composition;
 my %genomic_freqs; # storing the genomic sequence composition
 my %freqs;
 
-my $bismark_version = 'v0.21.0_dev';
+my $bismark_version = 'v0.22.0';
 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 = 'v0.21.0_dev';
+my $version = 'v0.22.0';
 my ($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) = process_commandline();
 
 ### only needed for bedGraph output

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 = 'v0.21.0';
+my $coverage2cytosine_version = 'v0.22.0';
 
 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) = process_commandline();
 

deduplicate_bismark

@@ -47,7 +47,7 @@ use Cwd;
 ### 26 03 2019
 ### Adapting to also work with softclipped reads (CIGAR operation S)
 
-my $dedup_version = 'v0.21.0_dev';
+my $dedup_version = 'v0.22.0';
 my @filenames;
 
 my ($single,$paired,$global_single,$global_paired,$samtools_path,$bam,$rrbs,$multiple,$output_dir,$outfile) = 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 = 'v0.21.0';
+my $filter_version = 'v0.22.0';
 my ($single,$paired);
 my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive,$percentage_cutoff,$minimum_count) = process_commandline();