Updates for new release

CHANGELOG.md

@@ -1,11 +1,20 @@
 # Bismark Changelog
 
-## Changelog for Bismark v0.24.1dev
+## Changelog for Bismark v0.24.1 (release on 29 May 2023)
 
-- Added new documentation website, built using [Material for Mkdocs](https://squidfunk.github.io/mkdocs-material/).
+- Added new [documentation website](http://felixkrueger.github.io/Bismark/), built using [Material for Mkdocs](https://squidfunk.github.io/mkdocs-material/). Thanks to @ewels for a great (late-night) effort to break up and restructure what had become a fairly unwieldy monolithic beast
 
 - Added documentation for cytosine context summary, useful for `GpC` methylation or filtering for specific C context (e.g. `CpA`)
 
+- Updated docs for the dovetailing 
+
+
+### Bismark
+- Warning messages for closing ambiguous and unmapped filehandles only occur when these options were specified [see here](https://github.com/FelixKrueger/Bismark/commit/1e86f6473415b5f95ba686f93efab7aa70c7bb86)
+
+
+
+
 ## Changelog for Bismark v0.24.0 (Release on 07 October 2022)
 
 ### Bismark

NOMe_filtering

@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -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 = 'v0.24.0';
+my $nome_version = 'v0.24.1';
 
 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();
 

README.md

@@ -24,7 +24,7 @@ Bismark is written in Perl and is executed from the command line. To install Bis
 
 Bismark needs the following tools to be installed and ideally available in the `PATH` environment:
 
-- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/) or [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml)
+- [Bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/) or [HISAT2](https://ccb.jhu.edu/software/hisat2/index.shtml) or [minimap2](https://lh3.github.io/minimap2/minimap2.html)
 - [Samtools](http://www.htslib.org/)
 
 ## Links

bam2nuc

@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -31,7 +31,7 @@ my %freqs;   # keeping a record of which chromosomes have been processed
 my %genomic_freqs;
 my %processed;
 
-my $bam2nuc_version = 'v0.24.0';
+my $bam2nuc_version = 'v0.24.1';
 
 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 = 'v0.24.0dev';
+my $bismark_version = 'v0.24.1';
 my $copyright_dates = "2010-23";
 
 my $start_run = time();

bismark2bedGraph

@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -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 = 'v0.24.0';
+my $bismark2bedGraph_version = 'v0.24.1';
 
 my @bedfiles;
 my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total

bismark2report

@@ -5,7 +5,7 @@ use Getopt::Long;
 use FindBin qw($RealBin);
 use lib "$RealBin/../lib";
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -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 = 'v0.24.0';
+my $bismark2report_version = 'v0.24.1';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();

bismark2summary

@@ -5,7 +5,7 @@ use Getopt::Long;
 use FindBin qw($RealBin);
 use lib "$RealBin/../lib";
 
-## This program is Copyright (C) 2010-22, Felix Krueger <[email protected]>.
+## This program is Copyright (C) 2010-23, Felix Krueger <[email protected]>.
 ## Thanks to Phil Ewels <[email protected]> (who wrote a first version of this
 ## script in 2013 or so when it was still 'legal' to use Highcharts.js (or maybe it 
 ## never was?....))
@@ -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 = '0.24.0';
+my $bismark_version = '0.24.1';
 
 # Last modified 09 11 2020
 

bismark_genome_preparation

@@ -6,7 +6,7 @@ use Getopt::Long;
 $|++;
 
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -42,8 +42,8 @@ my %genomic_freqs; # storing the genomic sequence composition
 my %freqs;
 
 
-my $bismark_version = 'v0.24.0';
-my $copyright_date = '2010-22';
+my $bismark_version = 'v0.24.1';
+my $copyright_date = '2010-23';
 my $last_modified = "19 May 2022";
 
 

bismark_methylation_extractor

@@ -8,7 +8,7 @@ use Carp;
 use FindBin qw($RealBin);
 use lib "$RealBin/../lib";
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -29,7 +29,7 @@ my $parent_dir = getcwd();
 
 my %fhs;
 
-my $version = 'v0.24.0';
+my $version = 'v0.24.1';
 my ($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

@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -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 = 'v0.24.0';
+my $coverage2cytosine_version = 'v0.24.1';
 
 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();
 

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 = 'v0.24.0';
+my $dedup_version = 'v0.24.1';
 my @filenames;
 
 my ($single,$paired,$global_single,$global_paired,$samtools_path,$bam,$rrbs,$multiple,$output_dir,$outfile,$parallel) = process_commandline();

docs/README.md

@@ -15,9 +15,9 @@ This User Guide outlines the Bismark suite of tools and gives more details for e
 
 Bismark is a set of tools for the time-efficient analysis of Bisulfite-Seq (BS-Seq) data. Bismark performs alignments of bisulfite-treated reads to a reference genome and cytosine methylation calls at the same time. Bismark is written in Perl and is run from the command line. Bisulfite-treated reads are mapped using the short read aligner Bowtie 2, or alternatively HISAT2. Therefore, it is a requirement that Bowtie 2 (or HISAT2) are also installed on your machine (see Dependencies).
 
-All files associated with Bismark as well as a test BS-Seq data set can be downloaded from [Babraham Bioinformatics](http://www.bioinformatics.babraham.ac.uk/projects/bismark/) or [Github](https://github.com/FelixKrueger/Bismark).
+All files associated with Bismark as well as a test BS-Seq data set can be downloaded from [Github](https://github.com/FelixKrueger/Bismark).
 
-We would like to hear your comments, suggestions or bugs about Bismark! Please e-mail them to: [[email protected]](mailto:[email protected])
+We would like to hear your comments, suggestions or bugs about Bismark! Please e-mail them to: [[email protected]](mailto:[email protected])
 
 ### Which kind of BS-Seq files are supported?
 
@@ -31,7 +31,7 @@ Bismark supports the alignment of bisulfite-treated reads (whole genome shotgun
 
 A full list of alignments modes can be found in [`Bismark_alignment_modes.pdf`](http://www.bioinformatics.babraham.ac.uk/projects/bismark/Bismark_alignment_modes.pdf).
 
-In addition, Bismark retains much of the flexibility of Bowtie 2 / HISAT2 (adjustable seed length, number of mismatches, insert size ...). For a full list of options please run:
+In addition, Bismark retains much of the flexibility of Bowtie 2 / HISAT2 / minimap2 (adjustable seed length, number of mismatches, insert size ...). For a full list of options please run:
 
 ```
 bismark --help
@@ -63,6 +63,6 @@ It should be stressed that the percent methylation value (context) is just a ver
 
 ## Credits
 
-Bismark was written by Felix Krueger at the [Babraham Bioinformatics Group](http://www.bioinformatics.babraham.ac.uk/).
+Bismark was written by Felix Krueger at the [Babraham Bioinformatics Group](http://www.bioinformatics.babraham.ac.uk/), now at Altos Labs, [Cambridge Institute](https://altoslabs.com/).
 
 ![Babraham Bioinformatics](images/bioinformatics_logo.png)

docs/bismark/filter_nonconverted_reads.md

@@ -50,4 +50,4 @@ Displays this help text end exits.
 
 Displays version information and exits.
 
-If you get stuck at any point or have any questions or comments please contact me via e-mail: [[email protected]](mailto:[email protected])
+If you get stuck at any point or have any questions or comments please contact me via e-mail: [[email protected]](mailto:[email protected])

docs/bismark/library_types.md

@@ -161,10 +161,10 @@ As we have seen before, the random priming of post-bisulfite methods (such as PB
 The same problems of random priming (indels, mispriming) will however most likely occur on both sides of the fragment to be sequenced, but it is doubtful that one would be able to spot these problems on the 3' end of reads because the problems would be expected on the 3' end of reads just before reading through into the adapter, and this may occur
 
 - at different positions in the read (depending on how short the fragment was)
-- at different positions within the read because of quality trimming in add`em`ition to adapter read-through contamination
+- at different positions within the read because of quality trimming in addition to adapter read-through contamination
 - not at all within the read length (whenever a fragment is longer than the sequenced read length)
 - at the 3' end even without hitting the adapter (i.e. just before the adapter)
 
 I guess there is a trade-off between accepting that a certain proportion of the reads may have a few biased biased positions towards their 5' ends, and preemptively trimming the 3' end by the same amount of bases as the 5' end. As a general rule it is probably safe to say that the shorter the average insert size of a library - the more of a problem the bias is. We have e.g. seen Pico Methyl libraries where ~80% of all fragments were shorter than 100bp, so a 2x125bp run would most likely be affected by the random priming bias on the 5' and 3' ends in nearly all fragments sequenced. We realise that trimming off say 10 bp from the 5' end and 3' end of a 100 bp read already removes 20% of the actually sequenced data, but this is the price you have to pay for using post-bisulfite kits...
 
-For these reasons we have put the _3' Trimming_ values in the table above in _(parentheses)_ as a reminder that you **should** probably perform 3' trimming of the data as well.
+For these reasons we have put the _3' Trimming_ values in the table above in _(parentheses)_ as a reminder that you **should** perform 3' trimming of the data as well.

filter_non_conversion

@@ -6,7 +6,7 @@ use Cwd;
 $|++;
 
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -22,7 +22,7 @@ $|++;
 ## along with this program. If not, see <http://www.gnu.org/licenses/>.
 
 my $parent_dir = getcwd();
-my $filter_version = 'v0.24.0';
+my $filter_version = 'v0.24.1';
 
 my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive,$percentage_cutoff,$minimum_count) = process_commandline();
 

methylation_consistency

@@ -3,7 +3,7 @@ use warnings;
 use strict;
 use Getopt::Long;
 
-my $VERSION = "0.24.0";
+my $VERSION = "0.24.1";
 my ($min_count,$global_single,$global_paired,$lower_threshold,$upper_threshold,$samtools_path,$chh) = process_commandline();
 
 if ($chh){