Kwalitee Issues

has_changelog

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

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

main_module_version_matches_dist_version

Make sure that the main module name and version are the same of the distribution.

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-1.132190/lib/Bio/Tradis/FilterTags.pm -- Around line 153: =over should be: '=over' or '=over positive_number' Around line 158: You forgot a '=back' before '=head2' Around line 160: =over should be: '=over' or '=over positive_number' Around line 165: You forgot a '=back' before '=head1' Bio-Tradis-1.132190/lib/Bio/Tradis/Map.pm -- Around line 84: =over should be: '=over' or '=over positive_number' Around line 89: You forgot a '=back' before '=head2' Around line 91: =over should be: '=over' or '=over positive_number' Around line 96: You forgot a '=back' before '=head1' Around line 98: =over should be: '=over' or '=over positive_number' Around line 116: You forgot a '=back' before '=head1' Bio-Tradis-1.132190/lib/Bio/Tradis/RemoveTags.pm -- Around line 113: =over should be: '=over' or '=over positive_number' Around line 118: You forgot a '=back' before '=head2' Around line 120: =over should be: '=over' or '=over positive_number' Around line 125: You forgot a '=back' before '=head1' Bio-Tradis-1.132190/lib/Bio/Tradis/RunTradis.pm -- Around line 423: =over should be: '=over' or '=over positive_number' Around line 432: You forgot a '=back' before '=head2' Around line 434: =over should be: '=over' or '=over positive_number' Around line 440: You forgot a '=back' before '=head1' Bio-Tradis-1.132190/lib/Bio/Tradis/TradisPlot.pm -- Around line 61: =over should be: '=over' or '=over positive_number' Around line 66: You forgot a '=back' before '=head1'

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.

has_meta_json

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

use_warnings

Add 'use warnings' (or its equivalents) to all modules, 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

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 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. metacpan
Bio::Tradis::Analysis::Exceptions metacpan
Bio::Tradis::Analysis::InsertSite metacpan
Bio::Tradis::CommandLine::AddTags Add given tags to the start of the sequence metacpan
Bio::Tradis::CommandLine::CheckTags Check for presence of tr tag in BAM file metacpan
Bio::Tradis::CommandLine::FilterFastqTags Remove given tags from the start of the sequence metacpan
Bio::Tradis::CommandLine::PlotTradis Generate plots as part of a tradis analysis metacpan
Bio::Tradis::CommandLine::RemoveFastqTags Remove given tags from the start of the sequence metacpan
Bio::Tradis::CommandLine::RunMapping Perform mapping metacpan
Bio::Tradis::CommandLine::TradisAnalysis Perform full tradis analysis metacpan
Bio::Tradis::CommandLine::TradisBam Adds tags to sequences if tags are present metacpan
Bio::Tradis::DetectTags Detect tr tags in BAM file metacpan
Bio::Tradis::FilterTags Filter tags in a fastq file metacpan
Bio::Tradis::Map Perform mapping metacpan
Bio::Tradis::Parser::Bam Very basic BAM parser. Limited functionality. metacpan
Bio::Tradis::Parser::Fastq Basic FastQ parser. metacpan
Bio::Tradis::RemoveTags Remove tags from seqs a fastq file metacpan
Bio::Tradis::RunTradis Perform all steps required for a tradis analysis metacpan
Bio::Tradis::TradisPlot Generate plots as part of a tradis analysis metacpan

Other Files

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