Updating files for release 0.20.1

FelixKrueger · Feb 1, 2019 · db275a3 · db275a3
1 parent 4f3d249
commit db275a3
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Showing 11 changed files with 46 additions and 35 deletions.
diff --git a/NOMe_filtering b/NOMe_filtering
@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-18, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-19, 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 = 'v0.20.0';
+my $nome_version = 'v0.20.1';
 
 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();
 
@@ -432,7 +432,7 @@ sub process_commandline{
 
                 Bismark NOMe_filtering, Version: $nome_version
 
-          Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+          Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
 	    www.bioinformatics.babraham.ac.uk/projects/bismark/
                   https://github.com/FelixKrueger/Bismark
 

diff --git a/bam2nuc b/bam2nuc
@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-18, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-19, 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 = 'v0.20.0';
+my $bam2nuc_version = 'v0.20.1';
 
 my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline();
 
@@ -380,8 +380,10 @@ sub process_commandline{
                                      bam2nuc
 
                            Bismark Version: $bam2nuc_version
-              Copyright 2010-16 Felix Krueger, Babraham Bioinformatics
+              Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
                 www.bioinformatics.babraham.ac.uk/projects/bismark/
+                     https://github.com/FelixKrueger/Bismark
+	       
 
 
 VERSION
@@ -650,7 +652,7 @@ TT      5055    10.96   1314144 10.80   0.004
 
 This file is picked up and plotted by bismark2report automatically if found in the folder.
 
-                              Script last modified: 26 April 2018
+                              Script last modified: 07 Dec 2018
 
 EOF
     ;

diff --git a/bismark b/bismark
@@ -25,7 +25,7 @@ use lib "$RealBin/../lib";
 
 
 my $parent_dir = getcwd();
-my $bismark_version = 'v0.20.0_dev';
+my $bismark_version = 'v0.20.1';
 my $start_run = time();
 # warn "Run started at: $start_run\n";
 my $command_line = join (" ",@ARGV);
@@ -7809,7 +7809,7 @@ sub process_command_line{
           Bismark - Bisulfite Mapper and Methylation Caller.
 
                        Bismark Version: $bismark_version
-        Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+        Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
               www.bioinformatics.babraham.ac.uk/projects/
                 https://github.com/FelixKrueger/Bismark
 
@@ -7825,6 +7825,7 @@ VERSION
 
   if ($bowtie1){
     $bowtie2 = 0;
+    warn ">>> Please note that the use of Bowtie 1 is now deprecated. Bowtie 1 support will be removed from the Bismark suite in due course. <<<\n"; sleep(3);
   }
   else{ # Bowtie 2 is now the default mode (as of 27 July 2015)
     $bowtie2 = 1;
@@ -10207,7 +10208,8 @@ BOWTIE 2 SPECIFIC OPTIONS
 
 --bowtie1                Uses Bowtie 1 instead of Bowtie 2, which might be a good choice for faster and very short
                          alignments. Bismark assumes that raw sequence data is adapter and/or quality trimmed where
-                         appropriate. Default: off.
+                         appropriate. Default: off. PLEASE NOTE: that the use of Bowtie 1 is now deprecated. Bowtie 1
+                         support will be removed from the Bismark suite in due course.
 
 --bowtie2                Default: ON. Uses Bowtie 2 instead of Bowtie 1. Bismark limits Bowtie 2 to only perform end-to-end
                          alignments, i.e. searches for alignments involving all read characters (also called

diff --git a/bismark2bedGraph b/bismark2bedGraph
@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-18, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-19, 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 = 'v0.20.0';
+my $bismark2bedGraph_version = 'v0.20.1';
 
 my @bedfiles;
 my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total
@@ -626,7 +626,7 @@ sub process_commandline{
                                 bismark2bedGraph
 
                       Bismark Extractor Version: $bismark2bedGraph_version
-              Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+              Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
                 www.bioinformatics.babraham.ac.uk/projects/bismark/
                      https://github.com/FelixKrueger/Bismark
 

diff --git a/bismark2report b/bismark2report
@@ -5,7 +5,7 @@ use Getopt::Long;
 use FindBin qw($RealBin);
 use lib "$RealBin/../lib";
 
-## This program is Copyright (C) 2010-18, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-19, 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 = 'v0.20.0';
+my $bismark2report_version = 'v0.20.1';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();
@@ -81,7 +81,7 @@ while (@alignment_reports){
   }
 
 
-  # Creation timestamp
+  # Create timestamp
   $doc = getLoggingTime($doc);
 
   # BISMARK ALIGNMENT REPORT (mandatory)
@@ -1017,7 +1017,7 @@ sub read_report_template{
 	$doc .= $_."\n";
     }
 
-    close DOC or die $!;
+    close DOC or warn $!;
     return $doc;
 }
 
@@ -1066,7 +1066,7 @@ sub process_commandline{
                               Bismark HTML Report Module
 
                          bismark2report version: $bismark2report_version
-                     Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+                     Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
                        www.bioinformatics.babraham.ac.uk/projects/bismark/
                             https://github.com/FelixKrueger/Bismark
 

diff --git 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 <http://www.gnu.org/licenses/>.
-my $bismark_version = '0.20.0_dev';
+my $bismark_version = '0.20.1';
 
 # Last modified 03 01 2019
 

diff --git a/bismark_genome_preparation b/bismark_genome_preparation
@@ -6,7 +6,7 @@ use Getopt::Long;
 $|++;
 
 
-## This program is Copyright (C) 2010-18, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-19, 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
@@ -37,7 +37,7 @@ my $genomic_composition;
 my %genomic_freqs; # storing the genomic sequence composition
 my %freqs;
 
-my $bismark_version = 'v0.20.0_dev';
+my $bismark_version = 'v0.20.1';
 
 GetOptions ('verbose' => \$verbose,
 	    'help' => \$help,
@@ -62,8 +62,11 @@ if ($version){
           Bismark - Bisulfite Mapper and Methylation Caller.
 
           Bismark Genome Preparation Version: $bismark_version
-        Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+        Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
               www.bioinformatics.babraham.ac.uk/projects/
+               https://github.com/FelixKrueger/Bismark
+	      
+
 
 VERSION
   exit;
@@ -108,6 +111,8 @@ if ($bowtie1){
     }
     $bowtie2 = 0;
     $verbose and print "Aligner to be used: Bowtie (1)\n";
+
+    warn "Please note that the use of Bowtie 1 is now deprecated. Bowtie 1 support will be removed from the Bismark suite in due course.\n"; sleep(3);
 }
 else{ # Bowtie 2 is now the default mode (as of 27 July 2015)
     if ($bowtie2){
@@ -492,8 +497,7 @@ sub create_bisulfite_genome_folders{
       die "The specified genome folder $genome_folder does not contain any sequence files in FastA format (with .fa, .fa.gz, .fasta or .fasta.gz file extensions)\n";
   }
 
-  warn "Bisulfite Genome Indexer version $bismark_version (last modified 25 September 2018)\n";
-  sleep (1);
+  warn "Bisulfite Genome Indexer version $bismark_version (last modified 01 February 2019)\n";
 
   # creating a directory inside the genome folder to store the bisfulfite genomes unless it already exists
   my $bisulfite_dir = "${genome_folder}Bisulfite_Genome/";
@@ -634,6 +638,8 @@ two simultaneous instances of the Bowtie 1 or 2 indexer (bowtie-build or bowtie2
 that the indexing process can take up to several hours; this will mainly depend on genome size
 and system resources.
 
+>>> PLEASE NOTE THAT USING BOWTIE 1 IS NOW DEPRECATED, AND WILL BE REMOVED FROM BISMARK IN FUTURE VERSIONS <<<
+
 
 
 The following is a brief description of command line options and arguments to control the
@@ -657,7 +663,8 @@ OPTIONS:
 
 --bowtie2                This will create bisulfite indexes for Bowtie 2. (Default: ON).
 
---bowtie1                This will create bisulfite indexes for Bowtie 1. (Default: OFF).
+--bowtie1                This will create bisulfite indexes for Bowtie 1. (Default: OFF). PLEASE NOTE THAT USING
+                         BOWTIE 1 IS NOW DEPRECATED, AND WILL BE REMOVED FROM BISMARK IN FUTURE VERSIONS. 
 
 --parallel INT           Use several threads for each indexing process to speed up the genome preparation step.
                          Remember that the indexing is run twice in parallel already (for the top and bottom strand
@@ -686,6 +693,6 @@ ARGUMENTS:
                          (with the file extension: .fa or .fasta (also ending in .gz)). Specifying this path is mandatory.
 
 
-This script was last modified on 25 September 2018.
+This script was last modified on 01 February 2019.
 HOW_TO
 }
diff --git a/bismark_methylation_extractor b/bismark_methylation_extractor
@@ -29,7 +29,7 @@ my $parent_dir = getcwd();
 
 my %fhs;
 
-my $version = 'v0.20.0_dev';
+my $version = 'v0.20.1';
 my ($ignore,$genomic_fasta,$single,$paired,$full,$report,$no_overlap,$merge_non_CpG,$vanilla,$output_dir,$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
@@ -1003,7 +1003,7 @@ sub process_commandline{
                            Bismark Methylation Extractor
 
                          Bismark Extractor Version: $version
-              Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+              Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
                 www.bioinformatics.babraham.ac.uk/projects/bismark/
                      https://github.com/FelixKrueger/Bismark
 

diff --git 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 = 'v0.20.0';
+my $coverage2cytosine_version = 'v0.20.1';
 
 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) = process_commandline();
 
@@ -1559,7 +1559,7 @@ sub process_commandline{
                                coverage2cytosine
 
                     Bismark coverage2cytosine Version: $coverage2cytosine_version
-              Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+              Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
                 www.bioinformatics.babraham.ac.uk/projects/bismark/
                     https://github.com/FelixKrueger/Bismark
 

diff --git a/deduplicate_bismark b/deduplicate_bismark
@@ -40,7 +40,7 @@ use Cwd;
 ### start and end at the exact same position
 ### Deduplication in --representative mode is now no longer supported. It wasn't what people should have wanted anyway
 
-my $dedup_version = 'v0.20.0';
+my $dedup_version = 'v0.20.1';
 my @filenames;
 
 my ($single,$paired,$global_single,$global_paired,$vanilla,$samtools_path,$bam,$rrbs,$multiple,$output_dir) = process_commandline();
@@ -1042,7 +1042,7 @@ sub process_commandline{
                   Bismark Deduplication Module
 
 	      Deduplicator Version: $dedup_version
-      Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+      Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
 	www.bioinformatics.babraham.ac.uk/projects/bismark/
 	    https://github.com/FelixKrueger/Bismark
   	  

diff --git a/filter_non_conversion b/filter_non_conversion
@@ -6,7 +6,7 @@ use Cwd;
 $|++;
 
 
-## This program is Copyright (C) 2010-18, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-19, 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 = 'v0.20.0';
+my $filter_version = 'v0.20.1';
 my ($single,$paired);
 my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive,$percentage_cutoff,$minimum_count) = process_commandline();
 
@@ -493,7 +493,7 @@ sub process_commandline{
                 	Bismark non-conversion filtering
 	    
                	    Bismark non-conversion version: $filter_version
-	    Copyright 2010-18 Felix Krueger, Babraham Bioinformatics
+	    Copyright 2010-19 Felix Krueger, Babraham Bioinformatics
                 www.bioinformatics.babraham.ac.uk/projects/bismark/
                     https://github.com/FelixKrueger/Bismark