Merge pull request #760 from FelixKrueger/dev

merging bclconvert fix

Author: FelixKrueger

CHANGELOG.md

@@ -1,9 +1,16 @@
 # Bismark Changelog
 
 
-## Changelog for Bismark v0.25.0 (release on 03 Aug 2025)
+## Changelog for Bismark v0.25.1 (release on 06 Aug 2025)
+
+### deduplicate_bismark
+
+- Also allowing the `+` sign as valid symbol when considering UMIs in `--bclconvert` mode [commit](268a8a26997f847c8e404f55cbdfb753a044190c)
 
 
+
+## Changelog for Bismark v0.25.0 (release on 03 Aug 2025)
+
 ### Bismark
 
 - now using 4 cores for merging multiple BAM files (more details [#707](https://github.com/FelixKrueger/Bismark/issues/707))

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 = 'v0.25.0';
+my $nome_version = 'v0.25.1';
 
 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();
 

bam2nuc

@@ -31,7 +31,7 @@ my %freqs;   # keeping a record of which chromosomes have been processed
 my %genomic_freqs;
 my %processed;
 
-my $bam2nuc_version = 'v0.25.0';
+my $bam2nuc_version = 'v0.25.1';
 
 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 = 'v0.25.0';
+my $bismark_version = 'v0.25.1';
 my $copyright_dates = "2010-25";
 
 my $start_run = time();

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 = 'v0.25.0';
+my $bismark2bedGraph_version = 'v0.25.1';
 
 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 = 'v0.25.0';
+my $bismark2report_version = 'v0.25.1';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();

bismark2summary

@@ -22,8 +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 = '0.25.0';
-
+my $bismark_version = '0.25.1';
 # Last modified 09 11 2020
 
 my ($report_basename,$page_title,$verbose) = process_commandline();

bismark_genome_preparation

@@ -42,7 +42,7 @@ my %genomic_freqs; # storing the genomic sequence composition
 my %freqs;
 
 
-my $bismark_version = 'v0.25.0';
+my $bismark_version = 'v0.25.1';
 my $copyright_date = '2010-25';
 my $last_modified = "19 May 2022";
 

bismark_methylation_extractor

@@ -27,9 +27,9 @@ my @filenames; # input files
 my %counting;
 my $parent_dir = getcwd();
 
-my %fhs;
+my %fhs;	
 
-my $version = 'v0.25.0';
+my $version = 'v0.25.1';
 my ($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

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 = 'v0.25.0';
+my $coverage2cytosine_version = 'v0.25.1';
 
 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();