Updated versions for release

FelixKrueger · May 15, 2017 · bc3f7f1 · bc3f7f1
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diff --git a/Docs/Bismark_User_Guide.html b/Docs/Bismark_User_Guide.html
@@ -35,14 +35,14 @@
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-<nav id="TOC"><ul><li><a href="#bismark-bisulfite-mapper">Bismark Bisulfite Mapper</a><ul><li><a href="#user-guide-v">User Guide - v0.17.0</a></ul></li><li><a href="#quick-reference">1) Quick Reference</a><ul><li><a href="#i-running-bismark-genome-preparation">(I) Running <code>bismark_genome_preparation</code></a></li><li><a href="#ii-running-bismark">(II) Running <code>bismark</code></a></li><li><a href="#iii-running-bismark-methylation-extractor">(III) Running <code>bismark_methylation_extractor</code></a></li><li><a href="#iv-running-bismark-report">(IV) Running <code>bismark2report</code></a></li><li><a href="#v-running-bismark-summary">(V) Running <code>bismark2summary</code></a></ul></li><li><a href="#bismark-general-information">2) Bismark - General Information</a><ul><li><a href="#what-is-bismark">What is Bismark?</a></li><li><a href="#installation-notes">Installation notes</a></li><li><a href="#dependencies">Dependencies</a></li><li><a href="#hardware-requirements">Hardware requirements</a></li><li><a href="#bs-seq-test-data-set">BS-Seq test data set</a></li><li><a href="#which-kind-of-bs-seq-files-are-supported">Which kind of BS-Seq files are supported?</a></li><li><a href="#how-does-bismark-work">How does Bismark work?</a></li><li><a href="#bismark-alignment-and-methylation-call-report">Bismark alignment and methylation call report</a></ul></li><li><a href="#running-bismark">3) Running Bismark</a><ul><li><a href="#i-bismark-genome-preparation">(I) Bismark Genome Preparation</a></li><li><a href="#ii-bismark-alignment-step">(II) Bismark Alignment Step</a></li><li><a href="#iii-bismark-methylation-extractor">(III) Bismark methylation extractor</a></li><li><a href="#iv-the-bismark-html-processing-report">(IV) The Bismark HTML Processing Report</a></li><li><a href="#v-the-bismark-summary-report">(V) The Bismark Summary Report</a></li><li><a href="#vi-bismark-nucleotide-coverage-report-bam-nuc">(VI) Bismark Nucleotide Coverage report (<code>bam2nuc</code>)</a></li><li><a href="#vii-filtering-out-non-bisulfite-converted-reads-filter-non-conversion">(VII) Filtering out non-bisulfite converted reads (<code>filter_non_conversion</code>)</a></li><li><a href="#viii-notes-about-different-library-types-and-commercial-kits">(VIII) Notes about different library types and commercial kits</a></ul></li><li><a href="#appendix-full-list-of-options">4) APPENDIX - Full list of options</a><ul><li><a href="#appendix-i-bismark-genome-preparation">Appendix (I): Bismark Genome Preparation</a></li><li><a href="#appendix-ii-bismark">Appendix (II): Bismark</a></li><li><a href="#appendix-iii-bismark-methylation-extractor">Appendix (III): Bismark Methylation Extractor</a></li><li><a href="#appendix-iv-bismark-reports-for-the-test-data-set">Appendix (IV): Bismark reports for the test data set</a></ul></li><li><a href="#credits">Credits</a></li></ul></nav>
+<nav id="TOC"><ul><li><a href="#bismark-bisulfite-mapper">Bismark Bisulfite Mapper</a><ul><li><a href="#user-guide-v">User Guide - v0.18.0</a></ul></li><li><a href="#quick-reference">1) Quick Reference</a><ul><li><a href="#i-running-bismark-genome-preparation">(I) Running <code>bismark_genome_preparation</code></a></li><li><a href="#ii-running-bismark">(II) Running <code>bismark</code></a></li><li><a href="#iii-running-bismark-methylation-extractor">(III) Running <code>bismark_methylation_extractor</code></a></li><li><a href="#iv-running-bismark-report">(IV) Running <code>bismark2report</code></a></li><li><a href="#v-running-bismark-summary">(V) Running <code>bismark2summary</code></a></ul></li><li><a href="#bismark-general-information">2) Bismark - General Information</a><ul><li><a href="#what-is-bismark">What is Bismark?</a></li><li><a href="#installation-notes">Installation notes</a></li><li><a href="#dependencies">Dependencies</a></li><li><a href="#hardware-requirements">Hardware requirements</a></li><li><a href="#bs-seq-test-data-set">BS-Seq test data set</a></li><li><a href="#which-kind-of-bs-seq-files-are-supported">Which kind of BS-Seq files are supported?</a></li><li><a href="#how-does-bismark-work">How does Bismark work?</a></li><li><a href="#bismark-alignment-and-methylation-call-report">Bismark alignment and methylation call report</a></ul></li><li><a href="#running-bismark">3) Running Bismark</a><ul><li><a href="#i-bismark-genome-preparation">(I) Bismark Genome Preparation</a></li><li><a href="#ii-bismark-alignment-step">(II) Bismark Alignment Step</a></li><li><a href="#iii-bismark-methylation-extractor">(III) Bismark methylation extractor</a></li><li><a href="#iv-the-bismark-html-processing-report">(IV) The Bismark HTML Processing Report</a></li><li><a href="#v-the-bismark-summary-report">(V) The Bismark Summary Report</a></li><li><a href="#vi-bismark-nucleotide-coverage-report-bam-nuc">(VI) Bismark Nucleotide Coverage report (<code>bam2nuc</code>)</a></li><li><a href="#vii-filtering-out-non-bisulfite-converted-reads-filter-non-conversion">(VII) Filtering out non-bisulfite converted reads (<code>filter_non_conversion</code>)</a></li><li><a href="#viii-notes-about-different-library-types-and-commercial-kits">(VIII) Notes about different library types and commercial kits</a></ul></li><li><a href="#appendix-full-list-of-options">4) APPENDIX - Full list of options</a><ul><li><a href="#appendix-i-bismark-genome-preparation">Appendix (I): Bismark Genome Preparation</a></li><li><a href="#appendix-ii-bismark">Appendix (II): Bismark</a></li><li><a href="#appendix-iii-bismark-methylation-extractor">Appendix (III): Bismark Methylation Extractor</a></li><li><a href="#appendix-iv-bismark-reports-for-the-test-data-set">Appendix (IV): Bismark reports for the test data set</a></ul></li><li><a href="#credits">Credits</a></li></ul></nav>
 <h1 id="bismark-bisulfite-mapper">Bismark Bisulfite Mapper</h1>
 
 <p><img title="Bismark" id="header_img" src="Images/bismark.png"></p>
 
-<h2 id="user-guide-v">User Guide - v0.17.0</h2>
+<h2 id="user-guide-v">User Guide - v0.18.0</h2>
 
-<h4 id="january">18 January, 2017</h4>
+<h4 id="may">15 May, 2017</h4>
 
 <p>This User Guide outlines the Bismark suite of tools and gives more details for each individual step. For troubleshooting some of the more commonly experienced problems in sequencing in general and bisulfite-sequencing in particular please browse through the sequencing section at <a href="https://sequencing.qcfail.com/">QCFail.com</a>.</p>
 

diff --git a/NOMe_filtering b/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 = 'v0.17.1_dev';
+my $nome_version = 'v0.18.0';
 
 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();
 

diff --git a/bam2nuc b/bam2nuc
@@ -31,7 +31,7 @@ my %freqs;   # keeping a record of which chromosomes have been processed
 my %genomic_freqs;
 my %processed;
 
-my $bam2nuc_version = 'v0.17.0_dev';
+my $bam2nuc_version = 'v0.18.0';
 
 my ($output_dir,$genome_folder,$parent_dir,$samtools_path,$genome_freq_only) = process_commandline();
 

diff --git a/bismark b/bismark
@@ -25,7 +25,7 @@ use lib "$RealBin/../lib";
 
 
 my $parent_dir = getcwd();
-my $bismark_version = 'v0.17.1_dev';
+my $bismark_version = 'v0.18.0';
 my $start_run = time();
 # warn "Run started at: $start_run\n";
 my $command_line = join (" ",@ARGV);

diff --git a/bismark2bedGraph b/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 = 'v0.17.0';
+my $bismark2bedGraph_version = 'v0.18.0';
 
 my @bedfiles;
 my @methylcalls = qw (0 0 0); # [0] = methylated, [1] = unmethylated, [2] = total

diff --git a/bismark2report b/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 = 'v0.17.1_dev';
+my $bismark2report_version = 'v0.18.0';
 my (@alignment_reports,@dedup_reports,@splitting_reports,@mbias_reports,@nuc_reports);
 
 my ($output_dir,$verbose,$manual_output_file) = process_commandline();

diff --git a/bismark2summary b/bismark2summary
@@ -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 $bismark_version = '0.17.1_dev';
+my $bismark_version = '0.18.0';
 
 # Last modified 24 02 2017
 

diff --git a/bismark_genome_preparation b/bismark_genome_preparation
@@ -36,7 +36,7 @@ my $genomic_composition;
 my %genomic_freqs; # storing the genomic sequence composition
 my %freqs;
 
-my $bismark_version = 'v0.17.0';
+my $bismark_version = 'v0.18.0';
 
 GetOptions ('verbose' => \$verbose,
 	    'help' => \$help,

diff --git a/bismark_methylation_extractor b/bismark_methylation_extractor
@@ -29,7 +29,7 @@ my $parent_dir = getcwd();
 
 my %fhs;
 
-my $version = 'v0.17.1_dev';
+my $version = 'v0.18.0';
 my ($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,$multicore,$yacht) = process_commandline();
 
 

diff --git a/copy_bismark_files_for_release.pl b/copy_bismark_files_for_release.pl
@@ -13,7 +13,7 @@
   mkdir $dir or die "Failed to create directory: $!\n\n";
 }
 
-my @files = ('RELEASE_NOTES.md','bismark','bismark_genome_preparation','bismark_methylation_extractor','bismark2bedGraph','bismark2report','coverage2cytosine','license.txt','RRBS_Guide.pdf','deduplicate_bismark','bam2nuc','bismark2summary','filter_non_conversion');
+my @files = ('CHANGELOG.md','bismark','bismark_genome_preparation','bismark_methylation_extractor','bismark2bedGraph','bismark2report','coverage2cytosine','license.txt','RRBS_Guide.pdf','deduplicate_bismark','bam2nuc','bismark2summary','filter_non_conversion','NOMe_filtering');
 
 my @reporting = ('bismark_sitrep.js','bismark_sitrep.tpl','highcharts.js','jquery-3.1.1.min.js');
 
@@ -66,7 +66,7 @@ sub copy_docs_and_warn{
 ### SETTING PERMISSIONS
 #######################
 
-@files = ('bismark','bismark_genome_preparation','bismark_methylation_extractor','bismark2bedGraph','bismark2report','coverage2cytosine','deduplicate_bismark','bam2nuc','bismark2summary','filter_non_conversion');
+@files = ('bismark','bismark_genome_preparation','bismark_methylation_extractor','bismark2bedGraph','bismark2report','coverage2cytosine','deduplicate_bismark','bam2nuc','bismark2summary','filter_non_conversion','NOMe_filtering');
 
 foreach my $file (@files){
   set_permissions($file);

diff --git a/coverage2cytosine b/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 = 'v0.17.0_dev';
+my $coverage2cytosine_version = 'v0.18.0';
 
 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) = process_commandline();
 

diff --git a/deduplicate_bismark b/deduplicate_bismark
@@ -32,7 +32,7 @@ use Getopt::Long;
 ### 16 09 2016
 ### to detect paired-end command from the @PG line we now allow -1 and -2 or --1 and --2 (or a combination thereof)
 
-my $dedup_version = 'v0.17.0';
+my $dedup_version = 'v0.18.0';
 
 my $help;
 my $representative;

diff --git a/filter_non_conversion b/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 = 'v0.17.1_dev';
+my $filter_version = 'v0.18.0';
 my ($single,$paired);
 my ($global_single,$global_paired,$samtools_path,$threshold,$consecutive) = process_commandline();