Updated Documentation for release v0.15.0

RELEASE_NOTES.txt

@@ -60,7 +60,8 @@ and CX_report output files (and thus not with the option --gc or --split_files.
 is now also passed on from the bismark_methylation_extractor.
 
 Added a check to coverage2cytosine to bail if no information was found in the coverage file, e.g. if
-a wroong file path for a cov.gz file had been specified.
+a wrong file path for a cov.gz file had been specified.
+
 
 bismark2bedGraph
 ================

bismark

@@ -24,7 +24,7 @@ use Getopt::Long;
 
 
 my $parent_dir = getcwd;
-my $bismark_version = 'v0.14.6_dev';
+my $bismark_version = 'v0.15.0';
 my $command_line = join (" ",@ARGV);
 
 
@@ -9829,11 +9829,11 @@ Output:
                          the SAM output will be compressed with GZIP instead (yielding a .sam.gz output file).
 
 --cram                   Writes the output to a CRAM file instead of BAM. This requires the use of Samtools 1.2 or higher.
-                         This mode is currently developmental and does not work in --multicore mode.
-
---cram_ref <ref_file>    CRAM output requires you to specify a reference genome as a single FastA file. Currently you need
-                         to provide this file yourself. Future versions will construct this file for you from the reference
-                         genome .fa sequences in case there were more than one.                 
+                         
+--cram_ref <ref_file>    CRAM output requires you to specify a reference genome as a single FastA file. If this single-FastA
+                         reference file is not supplied explicitly it will be regenerated from the genome .fa sequence(s)
+                         used for the Bismark run and written to a file called 'Bismark_genome_CRAM_reference.mfa' into the
+                         oputput directory.
 
 --samtools_path          The path to your Samtools installation, e.g. /home/user/samtools/. Does not need to be specified
                          explicitly if Samtools is in the PATH already.
@@ -10036,7 +10036,7 @@ Bismark SAM OUTPUT (default):
 Each read of paired-end alignments is written out in a separate line in the above format.
 
 
-Last edited on 08 Jan 2016.
+Last edited on 14 Jan 2016.
 
 HOW_TO
 }

bismark2bedGraph

@@ -6,7 +6,7 @@ use Getopt::Long;
 use Cwd;
 use Carp;
 
-## This program is Copyright (C) 2010-15, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-16, 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 = 'v0.14.6';
+my $bismark2bedGraph_version = 'v0.15.0';
 
 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($Bin);
 use lib "$Bin/../lib";
 
-## This program is Copyright (C) 2010-15, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-16, 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 "$Bin/../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 = 'v0.14.3';
+my $bismark2report_version = 'v0.15.0';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();

bismark_genome_preparation

@@ -6,7 +6,7 @@ use Cwd;
 $|++;
 
 
-## This program is Copyright (C) 2010-15, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-16, 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
@@ -34,7 +34,7 @@ my $single_fasta;
 my $bowtie2;
 my $bowtie1;
 
-my $bismark_version = 'v0.14.6';
+my $bismark_version = 'v0.15.0';
 
 GetOptions ('verbose' => \$verbose,
 	    'help' => \$help,

bismark_methylation_extractor

@@ -29,7 +29,7 @@ my $parent_dir = getcwd();
 
 my %fhs;
 
-my $version = 'v0.14.6';
+my $version = 'v0.15.0';
 my ($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) = process_commandline();
 
 
@@ -5628,9 +5628,9 @@ DESCRIPTION
 
 The following is a brief description of all options to control the Bismark
 methylation extractor. The script reads in a bisulfite read alignment results file 
-produced by the Bismark bisulfite mapper and extracts the methylation information
-for individual cytosines. This information is found in the methylation call field
-which can contain the following characters:
+produced by the Bismark bisulfite mapper (in BAM/CRAM/SAM format) and extracts the
+methylation information for individual cytosines. This information is found in the
+methylation call field which can contain the following characters:
 
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        ~~~   X   for methylated C in CHG context                      ~~~
@@ -5901,7 +5901,7 @@ The genome-wide cytosine methylation output file is tab-delimited in the followi
 
 
 
-This script was last modified on 01 December 2015.
+This script was last modified on 14 January 2016.
 
 HOW_TO
 }

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 $coverage2cytosine_version = 'v0.14.6';
+my $coverage2cytosine_version = 'v0.15.0';
 
 my ($output_dir,$genome_folder,$zero,$CpG_only,$CX_context,$split_by_chromosome,$parent_dir,$coverage_infile,$cytosine_out,$merge_CpGs,$gc_context,$gzip) = process_commandline();