Kwalitee Issues

has_changelog

Add a Changelog (best named 'Changes') to the distribution. It should list at least major changes implemented in newer versions.

no_pod_errors

Remove the POD errors. You can check for POD errors automatically by including Test::Pod to your test suite.

Error: Bio-Tradis-1.3.0/lib/Bio/Tradis/CombinePlots.pm -- Around line 329: '=item' outside of any '=over'

use_strict

Add 'use strict' (or its equivalents) to all modules, or convince us that your favorite module is well-known enough and people can easily see the modules are strictly written.

Error: Bio::Tradis::Analysis::Exceptions, Bio::Tradis::Exception

has_meta_json

Add a META.json to the distribution. Your buildtool should be able to autogenerate it.

meta_yml_declares_perl_version

If you are using Build.PL define the {requires}{perl} = VERSION field. If you are using MakeMaker (Makefile.PL) you should upgrade ExtUtils::MakeMaker to 6.48 and use MIN_PERL_VERSION parameter. Perl::MinimumVersion can help you determine which version of Perl your module needs.

use_warnings

Add 'use warnings' (or its equivalents) to all modules (this will require perl > 5.6), or convince us that your favorite module is well-known enough and people can easily see the modules warn when something bad happens.

Error: Bio::Tradis::Analysis::Exceptions, Bio::Tradis::Exception

meta_yml_has_provides

Add all modules contained in this distribution to the META.yml field 'provides'. Module::Build or Dist::Zilla::Plugin::MetaProvides do this automatically for you.

Modules

Name Abstract Version View
Bio::Tradis Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. For more information on the TraDIS method, see http://genome.cshlp.org/content/19/12/2308 1.003000 metacpan
Bio::Tradis::AddTagsToSeq Takes a BAM file and creates a new BAM with tr and tq tags added to the sequence and quality strings. 1.003000 metacpan
Bio::Tradis::Analysis::Exceptions Custom exceptions 1.003000 metacpan
Bio::Tradis::Analysis::InsertSite Take in a bam file and plot the start position of each read 1.003000 metacpan
Bio::Tradis::CombinePlots Combine multiple plotfiles and generate updated statistics for the combined files 1.003000 metacpan
Bio::Tradis::CommandLine::AddTags Add given tags to the start of the sequence 1.003000 metacpan
Bio::Tradis::CommandLine::CheckTags Check for presence of tr tag in BAM file 1.003000 metacpan
Bio::Tradis::CommandLine::FilterFastqTags Remove given tags from the start of the sequence 1.003000 metacpan
Bio::Tradis::CommandLine::PlotCombine Combine multiple plotfiles and generate updated statistics for the combined files 1.003000 metacpan
Bio::Tradis::CommandLine::PlotTradis Generate plots as part of a tradis analysis 1.003000 metacpan
Bio::Tradis::CommandLine::RemoveFastqTags Remove given tags from the start of the sequence 1.003000 metacpan
Bio::Tradis::CommandLine::RunMapping Perform mapping 1.003000 metacpan
Bio::Tradis::CommandLine::TradisAnalysis Perform full tradis analysis 1.003000 metacpan
Bio::Tradis::CommandLine::TradisBam Adds tags to sequences if tags are present 1.003000 metacpan
Bio::Tradis::DetectTags Detect tr tags in BAM file 1.003000 metacpan
Bio::Tradis::Exception Exceptions for input data 1.003000 metacpan
Bio::Tradis::FilterTags Filter tags in a fastq file 1.003000 metacpan
Bio::Tradis::Map Perform mapping 1.003000 metacpan
Bio::Tradis::Parser::Bam Very basic BAM parser. Limited functionality. 1.003000 metacpan
Bio::Tradis::Parser::Cigar Take in a cigar string and output start and end relative to the reference sequence 1.003000 metacpan
Bio::Tradis::Parser::Fastq Basic FastQ parser. 1.003000 metacpan
Bio::Tradis::RemoveTags Remove tags from seqs a fastq file 1.003000 metacpan
Bio::Tradis::RunTradis Perform all steps required for a tradis analysis 1.003000 metacpan
Bio::Tradis::Samtools Change samtools syntax depending on version found 1.003000 metacpan
Bio::Tradis::TradisPlot Generate plots as part of a tradis analysis 1.003000 metacpan

Other Files

MANIFEST metacpan
META.yml metacpan
Makefile.PL metacpan
README metacpan
README.md metacpan
dist.ini metacpan